We addressed the effects of phylogeny, ecology, and allometry on shape variation in ventral cranium, mandible and maxillary tooth-row in all five extant bandicoot rats. These rats are classified into two genera (Bandicota and Nesokia) and occupy different ecological niches along fossorial to aquatic gradient. The analysed structures are controlled by different gene loci, have diverse developmental patterns and different functional roles what induced us to hypothesize that they respond differently to the interplay between phylogenetic constrains and selective pressures. This was indeed the case in our results. Ventral cranial shape contained an apparent phylogenetic signal at various levels of taxonomic hierarchy of bandicoot rats and therefore accurately replicated the taxonomic hierarchy within the group. Molar crowns, which are less rich in anatomical complexity than the ventral cranium, provided a taxonomic grouping that was less straightforward in comparison with the skull. The phylogenetic signal was diluted in the mandible, probably by adaptive trends for the ecological niche. Unsurprisingly, an ecological gradient from a fossorial to aquatic ecotype explained 19.1% of mandibular shape variation. The major differences between ecotypes were on mandibular landmarks associated with insertion of major muscles that move the mandible during chisel-tooth drilling in fossorial B. bengalensis and N. indica. Among the three structures, the mandible was also the most affected by allometry, with size accounting for 14.0% of shape variability. Nesokia and Bandicota are by far the youngest murine taxa still attributed to a generic level. Small genetic differences however sharply contrast with unique shape features, evident in craniodental structures of these rats. This is particularly relevant for the endangered N. bunnii which is only known from a small range and peripheral isolate in Iraq. Morphological uniqueness emphasizes its ‘value’ in conservation policies more accurately than genetic metrics, making it more “visible” in a bunch of pest rats.