The evolution and ecomorphology of rodent craniomandibular apparatus have been extensively studied at a broad spatial scale. However, the question of how phenotypes and developmental instability interact with ecological pressures in human‐modified landscapes has been less explored. In this study, we test the influence of evolutionary history, diet, and habitat use on skull and mandible shape variation within a rodent community composed of eight cricetid species from an agroecosystem in central Argentina. We used geometric morphometrics, phylogenetic relationships, and ecological specializations in diet and habitat use to test the interplay between these factors. Our results indicated a strong phylogenetic signal for the symmetric components of the skull shape, but not for the mandible or asymmetric shapes. The strict insectivorous Oxymycterus rufus was the most phenotypically diverged within the rodent community. In general, more generalist species, both in terms of diet and habitat use, presented more phenotypic disparity (diversity) than specialists (e.g., strict insectivorous and natural and semi‐natural specialists) in craniomandibular shape variation. Dietary generalists and non‐strict granivores presented a tendency to show more skull asymmetric variation than non‐strict insectivores. These results suggest that generalist species exhibit higher levels of variation compared to specialist species, likely due to their wider range of responses to environmental stress. In cricetid species with similar ecological preferences, coexistence may thus be facilitated by morphological partitioning and developmental instability canalization based on dietary differences.