In the present study, the mycobiomes of two soils with different ecological conditions located in Benin (West Africa) were investigated by environmental sequencing (Illumina MiSeq) of the ITS2-region of ribosomal DNA to gain information about the influence of pedological stratification on fungal diversity. For each soil depth and horizon, fungal diversity and community composition were analyzed as well as the potential impact of site characteristics, like vegetation, on these traits. The retrieved sequences revealed in all their replicates high similarities between fungal communities of samples from the same site and soil horizon, but differed within one site in their horizons. It was possible to assign a saprotrophic, symbiotrophic, or parasitic lifestyle to 24% of the recorded fungal mOTUs. Plant parasites were found in all samples in similar proportions. The presence of ectomycorrhizal fungi in one site could be linked to the presence of ectomycorrhizal trees. Overall, it was observed that fungal diversity decreased with increasing depth if only one horizon was present, whereas a deeper horizon present at one site contained communities with a distinct composition regarding the taxonomical affiliations and lifestyles of the fungi found compared to the upper layer. Hence, soil horizonation seems to drive differences in the composition of fungal communities, and should be regarded with more attention when analyzing soil mycobiomes. Keywords: Benin; ectomycorrhiza; eDNA; fungi; fungal lifestyle; inselberg; lichens; soil fungi; soil horizons.