Coral reefs harbor among the highest biodiversity in marine ecosystems, with scleractinian corals forming complex symbiotic relationships with diverse invertebrates. Copepods are one of the most species-rich groups among coral-associated animals, yet their diversity remains poorly documented. Galaxea is a widespread reef-building coral genus in the Indo-Pacific, but its associated copepods have never been systematically surveyed.

In the South China Sea, Galaxea-associated copepods have been studied only at Dongsha Atoll, where Cheng and Dai (2018) reported two new species (Anchimolgus amplius and Xarifia dongshensis) and five new records (A. contractus, A. nasutus, A. tanaus, Clamocus spinifer, and Karanges hypsorophus), with Hemicyclops cyanus later added by Kim et al. (2025). These studies were based exclusively on morphology—no molecular data were linked to vouchers. The molecular framework was established by Mudrova (2018), who sampled 41 colonies from 11 Indo-Pacific localities and recovered 185 MOTUs, revealing high regional endemism.

We present the first integrative assessment of copepods associated with Galaxea in the South China Sea. Using a non-destructive DNA extraction protocol enabling one-to-one matching of sequences with morphological vouchers, we examined 121 specimens from Dongsha Atoll, Hainan, and Shenzhen. Morphology, combined with multi-gene markers (COI, ITS2, 18S) and species delimitation (ASAP, PTP, GMYC), revealed nine species (two with morphology only) belonging to two orders (Cyclopoida and Siphonostomatoida) and three families. Two species—Pseudanthessius oporinus and Hemicyclops parapiculus—are new records for the South China Sea, and the male of H. parapiculus is described for the first time. The three delimitation methods yielded congruent results, supporting seven MOTUs highly congruent with morphology. COI haplotype analysis of the dominant species, A. amplius, detected seven haplotypes, with males of different haplotypes differing in maxilliped setal ratio—a pattern reflecting either cryptic diversity or incipient geographic isolation (between Hainan and Dongsha), hypotheses requiring broader sampling and additional markers.

Our results provide the first DNA-linked morphological baseline for Galaxea-associated copepods in the South China Sea, filling a critical biogeographic gap in the Indo-Pacific. Species and haplotype compositions differ between Dongsha and Hainan—several species are shared, but haplotype distribution suggests restricted gene flow. Notably, A. amplius from Hainan exhibits morphological differences from Dongsha populations (e.g., maxilliped setal ratio), indicating possible regional differentiation. This study contributes fundamental data for biodiversity assessment and conservation of coral reef ecosystems in the region and offers a methodological framework applicable to other small symbiotic crustaceans.