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Global desert rodent communities were examined for evidence of phylogenetic and morphological community structure. Using geographical distribution data of desert rodents (within 15 assemblages), a composite molecular phylogeny and a geometric morphometric dataset of skulls, the mean pairwise distance and mean nearest taxon distance were calculated for each assemblage and compared with null communities. Community structure metrics detected phylogenetic clumping in two out of the 15 desert assemblages, indicating that co-occurring rodents were more closely related than expected by chance. No other assemblages showed a significant phylogenetic structure. Skull morphology had different structuring patterns, but overall, most examined desert assemblages were not significantly structured in skull morphology. Similar overall lack of community structure patterns was observed at the regional scale in both the phylogenetic and the body mass datasets. We also directly tested the association between phylogenetic and morphological structure and found it to be significant. The association between phylogenetic distance and increased diversity that we observed might indicate that niche partitioning facilities coexistence in diverse assemblages.