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The aim of the present study was to detect the heterogeneity of diversity in seasonal, site, tree species, and soil properties' effects on structural and functional attributes of the nematode communities under smooth mesquite, Prosopis laevigata and palo brea, Cericidium praecox within the Biosphere Reserve Valle de Tehuacán-Cuicatlán. Soils under biological crusts and neighbouring exposed sites were surveyed during the dry and wet seasons of 2018. Assessment of effective diversity (D) and diversity weighted by metabolic footprint (DMFP) were calculated as they reflect taxonomic and functional diversity. Trophic group abundances and both indices showed marked seasonal variation. Soil water content and bulk density were the only physicochemical variables that showed seasonal variation whereas bulk density, total C and total N content showed significant variation between soil under biological crusts and exposed sites. DMFP seemed to have a better chance of explaining a relationship with physicochemical heterogeneity than D as shown by PCA analyses. This places DMFP as an index for measuring diversity related to ecosystem services and therefore should be used as a tool for biological integrity assessments at the soil level and a support aid in stewardship soil management policies.