Based on an exemplar sample of pterostichine species (Carabidae: Pterostichini), 28S rDNA and COI and COII mtDNA sequence data are used to reconstruct a phylogenetic hypothesis for generic and subgeneric taxa putatively in or related to the subgenus Hypherpes Chaudoir (Coleoptera: Carabidae: Pterostichus Bonelli). The monophyly of Pterostichus is equivocal as the position of the subgenus Bothriopterus Chaudoir varies depending on methods of sequence alignment and gap region treatment. Pterostichus is found to be monophyletic in the combined data analysis if Cyclotrachelus Chaudoir and Tapinopterus Schaum are included in a larger concept of the genus. It is recommended that these be treated as subgenera of Pterostichus. Taxa currently included in Hypherpes are found to form a monophyletic group. No taxon previously suggested as a close relative of Hypherpes was found to be in, or closely related to Hypherpes. The sister-group of Hypherpes remains unclear, but there is some support for a clade of Pseudoferonina Ball Cryobius Chaudoir as the adelphotaxon. Taxa included in current classifications of Hypherpes compose a group that is in fact a complex of Hypherpes sensu stricto and two other subgenera, Leptoferonia Casey and Anilloferonia Van Dyke, which have been treated as junior synonyms of Hypherpes. Our analyses show that these three taxa are well supported as subgenera and reciprocally monophyletic, with the only change to previous taxonomic concepts of included species being the transfer of Pterostichus rothi (Hatch) from Anilloferonia to Leptoferonia. It is recommended that all three of these subgenera be recognized rather than being subsumed under Hypherpes. In Leptoferonia the DNA data support all species groups that were established by Hacker using morphological characters, with the exception of the inopinus-group. Significant reduction of the compound eyes has occurred independently at least five and possibly seven times in the Hypherpes complex. As many as five separate instances of eye reduction may have occurred in Leptoferonia alone. Maddison's concentrated changes test was used to show that there is a significant correlation between microphthalmy and autapomorphic sequence data as represented by longer than average terminal branch lengths based on Bayesian estimates of change per site. However, taxon pair contrasts show no consistent pattern of absolute difference of evolutionary rate or directionality of differences between small-eyed taxa and their sister species or sister clade. Repeated patterns of allopatric distributions are found for species-pairs of Leptoferonia, which consist of divisions along a north/south axis near the Pacific Coast and in the Sierra Nevada Range, or east/west divisions between coastal species and inland or Sierran species. In addition to allopatric biogeographic patterns, instances of sympatry in closely related species are interpreted to have been the result of two reduced-eye species moving into the deep litter and soil layer, thereby ecologically differentiating from near-surface leaf-litter and log dwelling species. Pterostichus morionides (Chaudoir), which is restricted to the Sierra Nevada Mountains in western North America, is found to be sister to P. adoxus (Say) and P. tristis (Dejean), the only species of Hypherpes in eastern North America. This grouping (mta-clade) was further tested by using a subset of taxa for 18S rDNA, CAD and wg sequence data and was found in some or all most-parsimonious trees for these data. In cases where they did not form a clade, they usually formed a convex group. Although counterintuitive due to the unusual disjunct biogeographic connection of these two areas and the generally dissimilar form of the adults, the mta-clade is very well supported by the DNA sequence data.