Understanding the ecological and historical causes and processes that shape biodiversity distribution patterns remains a challenging and fundamental task in biogeography, ecology, and evolution. To address this issue, taxonomic and phylogenetic β diversity can help us to assess the importance of ecological and historical factors that structure these biotic patterns. To make inferences about the processes underlying current spatial patterns in communities of Cricetidae across the state of Oaxaca, Mexico, their taxonomic and phylogenetic β diversity were assessed jointly. Our aims were: 1) to examine taxonomic and phylogenetic β diversity and their turnover and nestedness components among physiographic subprovinces; 2) to test for statistical significance of observed phylogenetic β diversity against the expected values of a null model; and 3) to evaluate if these metrics were correlated with geographical distance. We obtained the species composition for 12 subprovinces based on distribution models for 49 cricetid species present in Oaxaca, then carried out a maximum likelihood analysis to estimate their phylogenetic relationships. Our results show that the taxonomic and phylogenetic dissimilarities mainly were explained by the turnover component of species and lineages. In almost all pairwise comparisons, the null model approach revealed random patterns for phylogenetic β diversity values and its components. Mantel correlation models showed that the values of total taxonomic and phylogenetic diversity and their components are correlated with the geographical distances between subprovinces. Our results suggest that both taxonomic and phylogenetic β diversity are explained by the interplay between biogeographical history from southern Mexico, and the recent speciation processes in cricetid rodents. Given that speciation processes are allopatric for most cricetid taxa, the high values of spatial turnover can be explained by the small ranges of species, coupled with current abiotic conditions that act as filters, promoting specialization of species on particular conditions. Our results show the importance of the phylogenetic approach to unravel the multidimensional spatial patterns of biodiversity.