Most mesostigmatid mites (Arachnida: Parasitiformes) are soil-dwelling predators, feeding predominantly on detritivorous and fungivorous invertebrates. Little is known about the role of environmental and spatial parameters in driving the structure of their local communities. The aim of this study is to assess the relative importance of environmental/spatial parameters in different scales and microhabitats on the community structure of edaphic mesostigmatid mites in the southern Brazilian Atlantic Forest. Soil and litter samples were collected in 20 sites (six subsamples per microhabitat per site; N = 240 samples) distant from each other over ranges varying from 100 m to seven km. Geographic distances between sampling sites and spatial eigenfunctions were used as proxies of stochastic processes to assess the influence of spatial parameters on mite community structure. Environmental parameters included soil grain size, moisture and organic matter, vegetation structure, litter depth and percentage of leaves, branches, and thin roots in plant litter. We collected 1135 Mesostigmata individuals from 77 species/morphospecies. Mite composition strongly differed between soil and litter microhabitats. Mite communities geographically closer were more similar to each other in terms of Mesostigmata composition than expected if there is no spatial structure. Litter depth, soil organic matter and soil moisture significantly contributed to edaphic mite community structure. Deterministic processes predominated in explaining the composition of the litter fauna, while the composition of the soil fauna was more sensitive to stochastic processes. Our results provide evidence that the composition of Mesostigmata communities not only differ between microhabitats, but they are differently structured by environmental and spatial parameters depending on the scale. This provides new insight into the processes affecting of mite diversity within soil ecosystem at fine and broad scales, and highlights the importance of the spatial proximity and microhabitat in driving the composition of mite communities.