Thomasomys laniger and T. niveipes were described in the late 1800s from specimens taken in the Departamento de Cundinamarca (Cordillera Oriental of the Colombian Andes). These species are similar and T. niveipes subsequently was treated as a synomym of T. laniger. Recently T niveipes has been listed as a distinct species. We conducted karyological, morphological, and ecological analyses of specimens of both species, from the Carpanta Biological Reserve, Departamento de Cundinamarca. Our results indicate that T. niveipes is a species separate from T. laniger. Diploid numbers of chromosomes are 24 and 40, respectively. Fundamental numbers (FN) are similar. The two species differ morphologically in coloration of the hind foot (white in T. niveipes and dark in T. laniger), height of the cranium (greater in T. niveipes), and breadth of the interorbital region and breadth of the mesopterygoid fossa (both narrower in T. niveipes). We found T. laniger principally in forest habitat and T. niveipes in paramo. T. niveipes is known only from the departments of Cundinamarca and Boyacá at >2,900 m elevation.