Geological and paleobotanical data were used to construct an independent vicariance hypothesis ( = geographic cladogram) that attempted to predict patterns of micro- evolutionary differentiation among disjunct, coniferous forest populations of the Mexican woodrat Neotoma mexicana. The predictability of the geographic cladogram based on vicariance processes following the Pleistocene was tested by comparing the degree of congruence between the geographic cladogram and patterns of allozyme differentiation among disjunct populations. Results indicate that micro- evolutionary differentiation among allopatric populations exhibited a strong degree of congruence with the independent geographic model. Although fully resolved topologies of the geographic cladogram and a consensus tree constructed from allozymes were highly concordant (CI(1) = 0.917), topologies were not congruent in every respect. These data suggest that vicariance processes associated with dis- continuities in coniferous forest vegetation during the Pleistocene were a major factor structuring the pattern of differentiation among allopatric populations of woodrats in the American Southwest. Relict populations of N. mexicana also exhibited patterns of allozyme divergence that were consistent with the presence of the Rio Grande Valley as a major riverine barrier to dispersal. Indirect qualitative and quantitative estimates of gene flow (Nm = number of immigrants per generation) derived from allozymes suggest that late Pleistocene macro-habitats in the American Southwest affected genetic differentiation and gene flow among disjunct populations, particularly in the southern- most latitudes. Semi-desert grassland, chaparral and desert scrub appear to have functioned as major barriers to post- Pleistocene gene flow, whereas plains and Great Basin grass- land, and woodlands, appear to have functioned as respectively weaker barriers to immigration. Estimates of gene flow were lower among populations separated by woodlands than between those surrounded by continuous tracts of conif- erous forest. Viewed collectively, these data suggest a dy- namic interaction between the history of coniferous forest disjunctions, macro-habitat distribution and static geologic barriers associated with the unique landscape of the American