Gas hydrate systems are unique habitats for microorganisms in deep marine sediments, and gas hydrate reservoirs can be divided into focused high-flux and distributed low-flux gas hydrate systems. Little is known about the microbial distribution patterns in these systems, especially in the South China Sea (SCS). In this study, a macroscopic fracture filling gas hydrate zone (GHZ) and a microscopic pore filling GHZ, used as analogs to focused high-flux gas hydrate systems and distributed low-flux gas hydrate systems, were sampled and microbial diversity was investigated at Site GMGS2-16 in the northern SCS during the GMGS2 gas hydrate expedition based on high-throughput 16S rRNA gene sequencing. Compared to previous studies of the gas hydrate-bearing sites, high microbial diversity was observed in the sulfate methane transition zone (SMTZ) at Site GMGS2-16, and ANME-1b, a clade of anaerobic methanotrophic archaea (ANME), may mainly perform anaerobic oxidation of methane (AOM) in partnership with Desulfarculaceae and Desulfobacteraceae. For the GHZ (fracture-fill GHZ and pore-fill GHZ) and non-GHZ (SMTZ and Other, Other refers to the depth of 31.0-179.5mbsf), the bacterial richness indices (Shannon and inverse Simpson) revealed higher diversity in the GHZ than in the non-GHZ, while the archaeal richness indices showed a contrary pattern. Non-metric multidimensional scaling ordination revealed no significant differences in archaeal communities between the GHZ and non-GHZ, while differences between these zones were discovered in bacterial communities (P < .05), as the relative abundances of Bacilli and Clostridia (Phylum Firmicutes), Bacteroidia (Phylum Bacteroidetes), Alphaproteobacteria, Acidobacteria were significantly higher in the GHZ samples than in the non-GHZ samples. For the fracture-fill GHZ and pore-fill GHZ, the archaeal richness indices showed a higher diversity in the fracture-fill GHZ than in the pore-fill GHZ. High relative abundance of Hadesarchaea were found in the GHZ, especially in the pore-fill GHZ (accounting for 92.0–94.3% of the archaeal sequences), which might indicate Hadesarchaea play a vital role in the biogeochemical processes. For bacteria, the diversity indices were similar between the fracture-fill GHZ and the pore-fill GHZ, and no significant differences in bacterial communities were discovered between the two zones. Our study has provided new information for understanding the microbial diversity of the gas hydrate systems.