Deep subsurface microbial communities are more abundant in coarse-grained sedimentary rocks such as sandstones than in fine-grained mudstones. The low porosity and low permeability of mudstones are believed to restrict microbial life. Then, it is expected that distinct, isolated microbial communities may form in sandstones separated by mudstones. In this context, the connectivity between microbial communities in different sandstone units can be investigated to infer evolutionary patterns of diversification in space-time, which may potentially contribute with relevant data for analyses of hydraulic connectivity and stratigraphic correlation. In this work, we used high throughput DNA sequencing of a ribosomal 16S gene fragment to characterize the prokaryotic communities found in Permian sandstone samples of the same core that are separated by one mudstone interval, in the Charqueadas coal field, Parana Basin (Southern Brazil). Our samples were collected at ∌300 m deep, in porous sandstones separated by a thick mudstone package. Differences in the bacterial community structure between samples were observed for the classified OTUs, from phylum to genus. Molecular biology might be further applied as a possible tool to help to understand the spatial and temporal distribution of depositional facies, and the efficiency of low permeability rocks to compartmentalize reservoirs. Ongoing studies aim to extend the present investigation into further analyses regarding lateral changes in microbial communities present in the same sandstone units.