Indonesian coral reefs are the epicenter of marine biodiversity, yet are under rapid anthropogenically induced decline. Therefore, ecological monitoring of high diversity taxa is paramount to facilitate effective management and conservation. This study presents an initial report from a comprehensive survey of shallow-water (0–15 m) gorgonian assemblage composition and structure across sites with varying habitat quality within the Wakatobi Marine National Park (WMNP), SE Sulawesi, Indonesia. Current estimates of over 90 morphospecies from 38 genera and 12 families within the calcaxonian, holaxonian and scleraxonian groups are reported. This extensive survey confirms high local gorgonian abundance, diversity and species richness in the absence of anthropogenic influence and increasing with depth. Notably, morphological variants of the zooxanthellate species Isis hippuris Linnaeus, 1758, and Briareum Blainville, 1830, drive site and habitat assemblage differences across environmental gradients. Azooxanthellate taxa, particularly within the Plexauridae, drive species richness and diversity with depth. Of the 14 predictor variables measured, benthic characteristics, water flow and natural light explained just 30% of gorgonian assemblage structure. Furthermore, zooxanthellate and azooxanthellate taxa partitioned distinct gorgonian communities into two trophic groups—autotrophs and heterotrophs, respectively—with contrasting diversity and abundance patterns within and between study sites. This study strongly supports the WMNP as an area of high regional gorgonian abundance and diversity. Varying ecological patterns across environmental clines can provide the foundation for future research and conservation management strategies in some of the most biodiverse marine ecosystems in the world.
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