Understanding what drives morphological variation is important for both evolutionary biology and conservation. This study explores the factors influencing cranial size and shape variation in antelope ground squirrels (genus Ammospermophilus) by combining phylogenetic, allometric, ecological, and geographic perspectives. Geometric morphometric analyses were conducted on 58 cranial landmarks from 157 adult specimens representing four species (seven taxa) from 75 localities. Results show that species identity explains more cranial shape variation than allometry. However, after allometric correction, interspecific shape differences become nonsignificant, suggesting that species distinctions are mainly expressed through allometric effects. Ventral cranial shape shows a greater phylogenetic congruence and better distinguishes taxa (80% classification accuracy) than dorsal shape (66%), suggesting different evolutionary pressures across these cranial regions. Temperature, precipitation, and their seasonality explain >60% of environmental variation across species ranges, with Ammospermophilus leucurus uniquely exhibiting strong climate–shape covariation (r-PLS: 0.773-0.802). Geographically isolated taxa show increased morphological differentiation, with the insular A. l. insularis and peripheral A. nelsoni displaying the most divergent cranial morphologies. These results show that antelope squirrels’ cranial evolution is shaped by phylogeny, allometry, ecology, and geographic isolation. The marked morphological and genetic divergence of A. l. insularis and A. nelsoni, along with their limited ranges, and threatened status, makes them key conservation targets for maintaining phylogenetic diversity in this genus.