© 2020, Springer Nature Switzerland AG. Understanding the mechanisms that drive the assembly of communities is a central goal in ecology, and phylogenetic approaches allows for the testing of hypotheses related to such mechanisms. We analyzed assembly mechanisms of cricetid rodents in an environmentally heterogeneous region of southern Mexico by assessing their phylogenetic diversity and testing environmental predictors of the phylogenetic structure of local communities. We expected different assembly mechanisms among subprovinces according to their environmental heterogeneity. To test this, we obtained potential communities in cells of 100 km2 by overlapping potential distribution models of 49 species of cricetids. We also estimated a phylogenetic tree using sequences of Cytb obtained from GenBank and used null models to estimate the phylogenetic diversity of communities. We found two phylogenetic diversity patterns: overdispersion in lowlands and clustering in mountains. However, for the majority of the cells, the observed phylogenetic diversity does not differ from that of null models, suggesting that stochastic processes are the main drivers of the Cricetid communities. Only 25% of the communities located in the Sierra Madre de Oaxaca exhibited significant phylogenetic clustering, indicating that habitat filtering structures their composition. According to Generalized Additive Models, all environmental variables (elevation, temperature, precipitation, net primary productivity, and potential evapotranspiration) were highly significant predictors of phylogenetic diversity. Communities at lowest elevations and warmest temperatures showed the highest phylogenetic diversity values. Despite the role of environmental factors and low vagility of cricetids, our results showed that stochastic processes explained the assembly of communities more than deterministic ones, although in mountainous areas habitat filtering was also an outstanding mechanism. This study highlights the importance of including phylogenetic information to understand the mechanisms by which communities of small mammals are assembled.