- Coral reefs worldwide are being harmed through anthropogenic activities. Some coral reefs in Thailand remain well-preserved, including the shallow-coral reefs along Kra island, Nakhon Si Thammarat province. Interestingly, the microbial community in this environment remains unknown. The study thereby identified seasonal biodiversity of archaea, bacteria, fungi and small eukaryotes of 0.22-30 μm sizes, and their metabolic potentials, in this coral reef surface, using metagenomics with 16S and 18S rDNA pyrosequencing. Results showed species diversity and distribution that were different between the seasons, underlying by low Lennon and Yue & Clayton theta similarity indices (8.48-10.43% for 16S rDNA, 0.32-7.81% for 18S rDNA). The top most prokaryotic phylum for the summer was Proteobacteria (99.68%), whereas for the winter comprised mainly Proteobacteria (62.49%) and Bacteroidetes (35.88%). Uncultured bacteria in phyla Cyanobacteria, Planctomycetes, SAR406 and SBR1093 were also absent in the summer. For eukaryotic profiles, species belonging to animals were more common with great biodiversity in the summer, correlating with more animal activities in the summer. In contrast, in the winter, eukaryotic plant species were dominated and greatly diversified. Different structures of prokaryotic communities affected different metabolic subsystems between seasons: for examples, highly presence of desiccation stress functional group in the summer whereas more spore DNA protection functional group in the winter. Moreover, comparing the 16S rDNA profiles of these seasonal Kra reef surface against nowadays marine microbial databases indicated Kra reef surface prokaryotic profiles to be most resemblance to those of coastal Sichang island, Chonburi province, Thailand, and the 3 tropical GOS sites close to Galapagos island (GS039, GS040 and GS045), respectively. In conclusions, the study obtained metagenomic databases for marine prokaryotes and eukaryotes in summer and winter from Kra reef surface. The data helped understand seasonal dynamics of microbial diversity and metabolic potentials of this tropical ecosystem, and supported the knowledge for the world marine microbial biodiversity.