We tested the influence of migration and drift (isolation-by-distance model), and differences in micro-habitat on phenotypic traits, and correlated this with chromosomal polymorphism, at the intraspecific level, with geometric descriptors of the cranium and mandible over the entire range of subterranean rodent Ctenomys minutus. This species occurs in two different environments (dunes and sandy fields), along a strip extending for 470 km on the coastal plain of southern Brazil. Ctenomys minutus has seven parental chromosomal diploid numbers, several intraspecific hybrid zones, and up to 15 different karyotypes structured almost linearly along the coastline. Chromosomal populations show significant overall differences in size and shape, intraspecific hybrids are phenotypically intermediate between parental forms, and clustering suggests four groups delimited by chromosomal inversions and riverine barriers. Dune and field morphologies were significantly different in cranial shape. A significant but weak correlation between morphological and geographic distances along the complete distribution was found, supporting the isolation-by-distance model. The intraspecific phenotypic differences appear to arise as a combination of selection and drift acting as diversifying forces. Chromosomal inversions, rivers, and paleochannels appear to be acting as barriers to gene flow, unlike robertsonian fusions and fissions.