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. O desenvolvimento de metodos de analise citogenetica e molecular tem determinado um aumento da resolucao na distincao taxonomica entre formas cripticas. Entretanto, dados moleculares e geneticos sao geralmente oriundos de amostras pequenas e geograficamente restritas, frequentemente dificultando uma avaliacao objetiva de hipoteses alternativas a de distincao taxonomica, como a de que as diferencas resultem, de fato, de falhas na amostragem levando a descontinuidade de caracteres. E importante investigar essa possibilidade, especialmente quando envolve especies com distribuicao parapatrica e limites geograficos confusos. Nesse trabalho, analisamos padroes de variacao qualitativa e quantitativa na morfologia craniana em amostras populacionais de Cerradomys do Nordeste do Brasil. Essas series amostram um transecto norte-sul atraves dessa regiao, onde 2 especies com distribuicao parapatrica, C. vivoi e C . langguthi , sao atualmente reconhecidas. Nossos resultados mostram que os caracteres qualitativos considerados diagnosticos para cada especie variam gradualmente ao longo do transecto; da mesma forma, apesar da similaridade geral entre as amostras, as analises morfometricas revelaram um aumento no tamanho e modificacao gradual na forma do crânio das amostras do norte em direcao as amostras do sul. Apesar da distincao entre C. vivoi e C. langguthi ser suportada pela variacao cariologica e molecular disponivel, esses resultados sugerem que as 2 especies nao podem ser confiavelmente distintas somente com base em informacoes morfologicas, particularmente no que concerne as amostras das regioes intermediarias do transecto. Propomos um aumento na amostragem para essas regioes, alem do uso integrado de dados morfologicos, cariologicos e moleculares, de modo a possibilitar a deteccao de descontinuidades entre amostras populacionais e assim acessar os limites geograficos entre as especies reconhecidas desse genero.