[Background] Starfish is a kind of advanced echinoderm in Marine life, which contains abundant and bioactive resources of Symbiotic microorganisms. [Objective] The diversity of starfish symbiotic microorganisms in Naozhou island of Zhanjiang was analyzed. [Methods] Illumina MiSeq high-throughput sequencing technology was used to sequenced the 16S rRNA gene V3?V4 region and 18S rRNA gene ITS1?ITS2 region of bacteria and fungi respectively, and OTUs clustering analysis, Alpha diversity analysis and species classification analysis were conducted according to the sequencing results. [Results] The number of Filtered bacteria and fungi obtained by high-throughput sequencing is 61 992 and 71 196, and the number of OTUs is 2 384 and 529, respectively. According to the classification of species, the common bacteria are mainly Proteobacteria, whose average relative content is up to 77.37%, followed by Firmicutes、Bacteroidetes、Actinobacteria、Fusobacteria. Among dominant genus are Psychrobacter and Lactococcus; Symbiotic Fungi were mainly Ascomycota, with a relative content of 92.33%, followed by Fungi、Basidiomycota、Mortierellomycota and Rozellomycota. The dominant fungi genus was Pichia, followed by unclassified Candida. [Conclusion] There are abundant resources of symbiotic microorganisms in the starfish of Naozhou island, This study provides some reference for the researchers who are engaged in the sustainable development of starfish microbial resources and the excavation of bioactive substances in the future.