Average levels of protein heterozygosity (H̄ = 0.015) and polymorphism (P = 0.048) in 13 populations of Middle American pocket gophers (Orthogeomys, subgenus Macrogeomys) are unusually low by mammalian standards. This low genetic variability is attributed to subdivision of populations into small, isolated demes. Locus-by-locus and parsimony analyses of the protein data generally support retention of the currently recognized species of Macrogeomys. Phylogenetic analysis reveals that gross morphological similarities among highland pocket gophers (large body size and long pelage) and among lowland species (small body size and short pelage) are the result of evolutionary convergence. Most speciation in Macrogeomys appears to have occurred during the past 4.5 × 106 years, presumably influenced by Quaternary sea-level fluctuations that resulted in repeated fragmentations of geographic ranges of the species.