Mangrove forests contain some of the largest microbial diversities of any ecosystem on earth, trapping and cycling organic matter (OM) from land and sea. Studies on microorganisms in mangrove sediments have been almost entirely limited to the tropics; little is known about their counterparts in higher latitudes. While it is generally considered that diversity of macroorganisms increases toward the tropics, the trends and drivers of microbial diversity, particularly in intertidal systems, is poorly characterised. Although marine microbial diversity can change over latitudinal scales, terrestrial soil microorganisms generally change with soil physiochemical properties. In this study we sought to determine the drivers of bacterial and archaeal community structure in mangrove sediments along the West Australian (WA) coastline, and investigated the relative importance of latitude versus tidal position. Community structure was assessed in surface soils from four locations (tropical to temperate). We found that community structure was influenced by soil physiochemistry unique to each site and by tidal position, but not by latitude. Community structure was influenced by different factors depending on tidal position. In the low intertidal zone (fringe), community structure did not always differ along the latitudinal gradient, perhaps owing to frequent tidal inundation, as indicated by the higher proportion of similar marine microbial groups. Total Nitrogen and δ13C explained 34 % of the variation among the fringe microbial communities. δ13C does not commonly differentiate microbial communities in soils but, in the mangrove environment, it indicates the relative importance of marine vs terrestrial organic matter sources delivered to the fringe. In the high intertidal zone (scrub) community structure differed across all sites. Here, soil factors that commonly differentiate terrestrial soil microbial communities (pH, log OM, and C:N) explained 54 % of the variation among microbial communities. Therefore we expect to see microbial communities shift with OM inputs and pH in scrub soils, much like terrestrial soils, but uniquely shift with changing marine vs terrestrial inputs in fringe soils.