The evolutionary relationships of woodrats (Neotoma) were elulcidated through phylogenetic analyses of mitochondrial DNA restriction site and allozyme data. DNA samples from eleven nominal species from the genus Neotoma and two outgroup taxa, Ototylomys phyttotis and Xenomys nelsoni, were cleaved using a suite of 17 Type II restriction endonucleases. Mitochondrial DNA restriction profiles were visualized following electrophoresis of restriction digests via methods of Southern transfer and hybridization with 32P- and digoxigenin-labeled mtDNA probes. Restriction mapping resulted in the identification of 37 unique mtDNA haplotypes among the woodrat taxa examined. Proteins representing 24 presumptive structural gene loci were examined through starch gel electrophoresis. Binary-coded allozyme data and allozyme frequency data were analyzed using PAUP and FREQPARS, respectively. Phylogenetic analyses of the mtDNA restriction site data incorporated three different character type assumptions: unordered binary characters, Dollo characters, and differentially weighted unordered characters employing the STEPMATRIX option of PAUP. Proposed phylogenies for Neotoma are based on majority-rule consensus trees produced using bootstrap procedures. Phylogenetic analyses of the woodrat data sets revealed a distinct dichotomy among populations of white-throated woodrats (N. albigula) suggesting the presence of cryptic species within that taxon. MtDNA and allozyme data support the specific status of N. devia as distinct from N. lepida, and additionally reveal the presence of a third cryptic species referable to N. intermedia among the desert woodrats. Phylogenetic analyses of the genetic data also suggest subgeneric status for the desert woodrats, which is in agreement with evidence from morphology. The genetic data revealed a sister group relationship between N. stephensi and samples of N. mexicana, suggesting the placement of N. stephensi into the N. mexicana species-group. Neotoma fuscipes and N. cinerea formed a monophyletic lineage basal to the remaining members of the subgenus Neotoma which supports the assignment of N. fuscipes to the subgenus Teonoma with N. cinerea. Although stringent, Dollo parsimony methods produced the best supported phylogenies among the species of Neotoma. The STEPMATRIX approach was unable to resolve species relationships within species-groups but clearly delineated the higher taxonomic levels between species-groups and subgenera.