1. Numerous processes influence community structure. The relative importance of these processes are thought to vary with spatial, temporal, and taxonomic scale: density dependent interactions are thought to be most influential at small scales, at intermediate scales environmental conditions may be the most influential factor, and biogeographic processes are thought to be of greater importance at larger scales. Additionally, the stress-dominance hypothesis suggests that communities experiencing harsher environmental conditions will be predominantly structured by habitat filtering whereas communities experiencing more favorable conditions will be structured predominantly by density dependent interactions such as competition. 2. The aim of this study was to investigate the influence of environmental factors on phylogenetic community structure (PCS) of North American desert bats at multiple spatial and taxonomic scales. We also examined if the stress-dominance hypothesis is upheld in desert bats across an environmental gradient. 3. PCS metrics were calculated using species pools that differed in spatial (from all deserts to individual deserts) and taxonomic (all bat taxa, a single family, and a single genus) scale. We calculated mean temperature, precipitation, and seasonality for each site to determine if environmental gradients were related to degree of community structure. 4. At the largest spatial and taxonomic scales, communities were significantly phylogenetically clustered while degree of clustering decreased at the smallest spatial and taxonomic scales. Climatic data, particularly mean temperature and temperature seasonality, were important predictors of PCS at larger scales and under harsher conditions, but at smaller scales and in less stressful conditions there was a weaker relationship between PCS and climate. 5. This suggests that North American deserts, while harsh, are not uniform in the challenges they present to the faunas residing in them. Overall, the relationship between PCS and climatic data at large spatial and taxonomic scales, and in harsher conditions, suggests the influence of habitat filtering has been important in North American desert bat community assembly and that other processes have been important at smaller scales.