•The spatial diversity of bacterial and archaeal community in mangrove-inhabited mudflat is studied•Gradient variation of microbial community composition is found from high tidal flat to mid/low tidal flat•Stratified distribution of microbial communities is detected from surface to subsurface layer at a depth of 50 cm•The metabolism functions, such as photoautotrophy, sulfur-related respiration, and nitrification are varied in the profile•DO and DTN are the main physiochemical factors affecting the distribution of functional microbes in the mudflat Display omitted The gradient distribution of microbial communities has been detected in profiles along many natural environments. In a mangrove seedlings inhabited mudflat, the microbes drive a variety of biogeochemical processes and are associated with a dramatically changed environment across the tidal zones of mudflat. A better understanding of microbial composition, diversity and associated functional profiles in relation to physicochemical influences could provide more insights into the ecological functions of microbes in a coastal mangrove ecosystem. In this study, the variation of microbial community along successive tidal flats inhabited by mangrove seedlings were characterized based on the 16S rDNA gene sequences, and then the factors that shape the bacterial and archaeal communities were determined. Results showed that the tidal cycles strongly influence the distribution of bacterial and archaeal communities. Dissimilarity and gradient distribution of microbial communities were found among high tidal flat, mid-low tidal flat and seawater. Discrepancies were also as well observed from the surface to subsurface layers specifically in the high tidal flat. For example, Alphaproteobacteria displayed an increasing trend from low tidal to high tidal flat and vice versa for Deltaproteobacteria; Cyanobacteria and Thaumarchaeota were more dominant in the surface layer than the subsurface. In addition, by classifying the microorganisms into metabolic functional groups, we were able to identify the biogeochemical pathway that was dominant in each zone. The (oxygenic) photoautotrophy and nitrate reduction were enhanced in the mangrove inhabited mid tidal flat. It revealed the ability of xenobiotic metabolism microbes to degrade, transform, or accumulate environmental hydrocarbon pollutants in seawater, increasing sulfur-related respiration from high tidal to low tidal flat. An opposite distribution was found for major nitrogen cycling processes. The shift of both composition and function of microbial communities were significantly related to light, oxygen availability and total dissolved nitrogen instead of sediment types or salinity.