The spatial and geographic distribution of articles offers insight into the leading countries contributing to coral reef research in the South China Sea since 1999. A total of 45 regions have published articles in this field, with 42 of them forming part of a co-authorship network. Figure 2 illustrates the co-authorship network among these countries, where the size of each node represents the number of articles published by that region, and the thickness of the links reflects the strength of co-authorship ties between pairs of regions. Table 2 lists the top 10 regions ranked by the number of published articles, collaborating regions (number of links), total co-authored articles (total link strength), and the number of citations received.

As detailed in Table 2 , China leads across all four metrics, with 550 published articles, 33 collaboration links, 167 co-authorships, and 9,682 citations. While the second and third positions vary by metric, Taiwan, China ranks fourth with 60 articles, 23 collaborating countries, 77 co-authorships, and 1,445 citations. Malaysia follows in fifth place with 58 articles, 19 collaborating countries, 64 co-authorships, and 784 citations. Australia, the USA, Germany, Singapore, and the Netherlands are consistently among the top 10 contributors across all four metrics, though their specific rankings vary. As shown by the strength of the links in Figure 2 , China’s strongest collaborative ties are with the USA (38 co-authorships) and Australia (34 co-authorships), representing the most significant partnerships within the network.

Authors play a crucial role in evaluating the development of an academic field. A total of 2,661 authors have contributed to coral reef research in the South China Sea, with 112 authors having published at least five articles. Tables 3 and 4 list the most productive authors (based on the number of published articles) and the most influential authors (based on citation counts), respectively, along with their number of co-authors and co-authorships. According to these rankings, Yu Kefu is the most productive and influential author among the 2,661 contributors. Wang Yinghui ranks second in productivity and third in influence, while Huang Xueyong ranks third in productivity and second in influence.

Understanding the leading organizations in a specific research area can be achieved by analyzing inter-organizational collaborations. To identify the key research institutions, we listed the top 10 organizations with the highest number of publications ( Table 5 ) and created a co-authorship network map ( Figure 3 ) using VOSviewer. Among the top 10 organizations, eight are from China, while the remaining two are from Australia and Malaysia. The Chinese Academy of Sciences leads with 250 publications, followed by Guangxi University with 113 publications. The other organizations have published fewer than 100 papers. In terms of Citations Per Paper (CPP), University of Queensland, ranked eighth in total publications, holds the highest CPP at 51.2. Xiamen University ranks second with a CPP of 22.5, followed by Chinese Academy of Sciences with 21 CPP.

Figure 3 shows the co-authorship network of research organizations, where each node represents an organization, with the node size indicating the number of publications. The thickness of the connecting lines reflects the strength of collaboration between two organizations. The Chinese Academy of Sciences appears as the largest node, followed by the University of Chinese Academy of Sciences and the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou). The Chinese Academy of Sciences also has the strongest collaborative ties with other institutions, with its closest connection to the University of Chinese Academy of Sciences, followed by the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) and Guangxi University.

The 769 articles on coral reef research in the South China Sea within our dataset have been published in 275 journals. Among these, 42 journals have published at least five articles. Figures 4 and 5 present the top journals based on the number of published articles and citations, respectively. As shown in the figures, Science of the Total Environment leads in both the number of published articles and total citations. Frontiers in Marine Science ranks second in the number of published articles, while Marine Pollution Bulletin is the second most influential journal in terms of citations. Notably, there is a considerable gap between the second and third-ranked journals in both productivity and influence. Specifically, Science of the Total Environment and Frontiers in Marine Science have published 34 and 33 articles, respectively, while Marine Pollution Bulletin, the third-ranked journal in terms of productivity, has published 24 articles. Similarly, in terms of citations, Science of the Total Environment and Marine Pollution Bulletin have received 670 and 657 citations, respectively, which are significantly higher than the 479 citations received by Journal of Geophysical Research-Oceans. This highlights Science of the Total Environment as the leading journal in coral reef research in the South China Sea.

This section presents two primary analyses, focusing on the citations received by the articles and their bibliographic coupling.

The analysis of keyword frequency provides a basis for describing the research domain and the focus of the collected articles. After cleaning the keyword data, 2,179 unique keywords were identified, of which 112 appeared at least four times. A heat map of these 112 keywords, based on their frequencies, was generated using VOSviewer ( Figure 7 ). Since South China Sea and coral reef were part of the search query, they appear significantly more frequently than other terms and are therefore excluded from Figure 7 to allow for a clearer analysis of the research domain. Beyond these terms, the most frequently occurring keywords are coral, climate change, and coral bleaching, aligning with the research categories identified through the bibliographic coupling analysis. To facilitate the identification of the most frequent terms, author keywords with more than ten occurrences are listed in Table 8 .

Table 8 shows that most research has been conducted in the Xisha Islands, Malaysia, the Nansha Islands, Hainan, and the northern South China Sea. The primary research subjects are reflected in the keywords coral, coral reef fish, Scleractinian coral, diversity and coral community. The major research focus includes the negative impacts of climate change, macroalgae proliferation, sea level rise, and global warming, with coral bleaching identified as the most pressing issue. Regarding research methods, remote sensing emerges as the dominant approach. This technology enables detailed classification of complex reef benthic substrates and facilitates the investigation and assessment of coral reef health, driving significant progress in the field (Xu and Zhao, 2014). With rapid advancements in remote sensing data sources, spectral characteristics analysis, and recognition technologies, this method has gained increasing popularity. Its capacity for large-scale coverage and non-invasive monitoring makes it especially valuable for studying coral reef ecosystems (AlZayer et al., 2025; Huang et al., 2025; Liu et al., 2025).

The text mining analysis was conducted on the titles and abstracts of the collected peer-reviewed journal articles of our sample to uncover hidden semantic structures and research themes. After cleaning the data, 4134 unique noun phrases were identified. In order to base the analysis on the sufficiently frequent terms, a minimum of 5 occurrences was considered as a criterion for the selection of phrases, leading to the selection of 281 noun phrases. Then, the phrases were used to build clusters based on the co-occurrence of the terms to reveal the research themes of coral reef in the South China Sea. The 5 major theme identified includes (1) fundamental physical–biological interactions in reef systems, (2) biodiversity and symbiotic relationships in response to environmental stress, (3) climatic influences and the adaptive responses of reef systems, (4) conservation strategies and management practices for reef resilience, (5) remote sensing and algorithmic approaches for reef mapping and monitoring. Figure 8 presents the thematic structure of the coral reef research in the South China Sea. Similar to Figure 7 , the size of the circles and the links between them show the occurrence of identified terms and their co-occurrence, respectively.

The first thematic cluster focuses on fundamental physical–biological interactions in reef systems (Cluster #1). Keywords central to this research theme include “coral reef”, “island”, “ocean”, “water”, “sediment”, “model”, “dynamics”, “fish”, “organic-matter”, “calcification”. These terms reflect the interplay between physical factors—such as ocean currents, water characteristics, and sediment movement—and biological processes, like fish populations, organic matter cycling, and calcification (Wilson, 2008; Xu et al., 2011; Shao et al., 2017; Zhang et al., 2021; Fan et al., 2024). Overfishing has been found in Nansha Islands and in the Malaysian South China Sea, which causes the “coral reef crisis” (Bell et al., 2006; Arai, 2015; Zhang et al., 2021). Parrotfish play a crucial regulatory role in coral reef ecosystems, and their susceptibility to fishing activities could lead to a gradual transition towards algal dominance, resulting in ecological phase shifts (Wang et al., 2024). Models play a critical role in examining these interactions, offering insights into reef dynamics across different scenarios (Melbourne-Thomas et al., 2011). This cluster highlights the combined impact of geophysical and ecological processes on coral reef development and function.

The second research theme (Cluster #2) concentrates on biodiversity and symbiotic relationships in response to environmental stress. It encompasses concepts such as “diversity”, “patterns”, “temperature”, “reef”, “stress”, “zooxanthellae”, “connectivity”, and “microbial community”. Research indicates that richness, rarity, and phylogenetic diversity vary significantly among reef areas in the South China Sea, and outcomes following projected extinctions cannot be predicted by species diversity alone (Huang et al., 2016). In the South China Sea, corals exhibit varying patterns of adaptability: those in the southern region are primarily threatened by thermal stress, while northern corals often suffer from severe anthropogenic disturbances (Qin et al., 2020). Moreover, rising ocean temperatures have been widely linked to coral reef bleaching, typically marked by the expulsion of symbiotic zooxanthellae, loss of zooxanthellae pigmentation, or both (Li et al., 2008). Coral-associated bacterial communities, which are essential for coral ecosystems and holobiont health (Yu et al., 2021), undergo substantial structural changes during bleaching events (Yang et al., 2021). Collectively, these findings demonstrate how biodiversity and symbiotic interactions influence coral reef responses to environmental challenges, offering vital insights for developing effective conservation strategies.

The third thematic cluster explores climatic influences and the adaptive responses of reef systems (Cluster #3). Key terms such as “climate change”, “Great Barrier Reef”, “growth”, “variability”, “evolution”, “record”, “mortality”, and “ocean acidification” are central to this theme. Climate change affects coral reefs primarily through rising ocean temperatures and acidification, which may prevent some corals from surviving in tropical regions if they cannot adapt quickly enough (Yuan et al., 2019). Persistent seawater warming is recognized as a major threat to coral growth and reef development, with overall coral growth in the South China Sea projected to decline by the end of this century (Yan et al., 2019). The Great Barrier Reef, one of the most extensively studied coral reef systems, has provided research methodologies applicable to the South China Sea, such as the Foraminifera in Reef Assessment and Monitoring (FORAM) Index (A’ziz et al., 2021). Coral reefs in both the South China Sea and the Great Barrier Reef are experiencing declines, with mortality patterns in the Nansha area resembling those observed in the central Great Barrier Reef (Yu et al., 2012).

Conservation strategies and management practices for reef resilience (Cluster #4) have emerged as a leading research focus. The key terms in this theme are “community”, “impact”, “resilience”, “conservation”, “biodiversity”, “phase-shifts”, “assemblages”, “abundance”, “management”, “recovery”, “responses”, “coast”, and “coral cover”. Reefs in the South China Sea display spatial heterogeneity in resilience, recovery, and vulnerability to elevated water temperatures, as evidenced by variations in parameters such as coral cover and genus diversity. This variability necessitates targeted management interventions to guide reef rehabilitation for both biodiversity conservation and touristic development, involving relevant stakeholders (Vo et al., 2019). Notably, a phase shift from stony coral communities to alternative assemblages of octocorals and corallimorpharians has been observed in the South China Sea, attributed to outbreaks of crown-of-thorns starfish (Tkachenko et al., 2022). Reef restoration is recognized as an essential intervention to mitigate degradation. Moreover, these efforts have increased coastal community awareness of reef management and provided opportunities for active local participation and ownership (Chou et al., 2009).

The final thematic cluster highlights the application of remote sensing techniques and algorithmic approaches in reef mapping and monitoring (Cluster #5). Keywords associated with this research focus include “classification,” “depth,” “bathymetry,” “imagery,” “behavior,” “shallow waters,” “strength,” and “algorithm.” Shallow water depth estimation using multispectral imagery has become a vital method for marine surveying and mapping. To derive accurate bathymetric data, various algorithms such as the Quasi-Analytical Algorithm and geomorphic segmentation have been employed (Huang et al., 2017; Cheng et al., 2023; Zuo et al., 2024). Bathymetric data further support coral cover classification, enabling detailed assessment and monitoring of reef ecosystems (Asner et al., 2017). These advancements contribute to improved reef conservation and management strategies by enhancing the accuracy and efficiency of reef mapping efforts.