The advent of molecular and cytogenetic methodologies has improved our ability to recognize taxonomically distinctive, but morphologically cryptic forms. However, molecular and cytogenetic data are often based on small and geographically restricted samples, often hampering an objective evaluation of alternative hypotheses such as limited and/or uneven sampling leading to character discontinuity. It is important to investigate this alternative possibility, especially when it concerns species distributed parapatrically with confusing geographical limits. In this study, we analyze patterns of qualitative and quantitative variation in cranial morphology in a series of Cerradomys samples from northeastern Brazil. These samples form a north–south transect through this region, where 2 species with parapatric distributions, C. vivoi and C. langguthi, are currently recognized. Our results show that qualitative characters regarded as diagnostic for each species vary gradually along the transect and, despite the overall similarities among samples, cranial morphometric analysis reveals an increase in size and a gradual modification of skull shape from northern to southern samples. These findings indicate that, although the distinction between C. vivoi and C. langguthi is supported by available karyological and molecular variation, these 2 species cannot be confidently distinguished based only on morphology, particularly those samples from intermediate regions of the transect. We propose an intensification of sampling in these regions, and the integrated use of cytogenetic, molecular, and morphological data, in an attempt to refine the resolution of discontinuities among population samples and to access the geographical limits between the recognized species in this genus.