Electrophoretic variation in proteins encoded by 18 loci was analyzed in populations of Ctenomys differing in chromosome number (2n = 26 and 28). Intrapopulation and inter-population variation is high (P = 34.7%, H = 4%, S = 84%). Genetic distances are not consistently associated with differences in chromosome number. High Fis values suggest high levels of inbreeding or further population subdivision. The fixation index (Fst) is thought to reflect population fragmentation due to restricted vagility of the animals and historical chance events.