Species definitions are commonly based on documentation either of genetic or ecologic cohesion (biological species models) or of phylogenetic relationship (phylogenetic species concept). However, these philosophical positions are often incompatible with data on genealogical relationship of and genetic/reproductive interactions among member populations. The difficulty in defining species in nature based on either viewpoint is exacerbated when times between divergence events are short, when differentiation among populations prior to speciation is extensive, and when reticulation events persist subsequent to speciation. We illustrate this set of problems with data on mitochondrial DNA sequences and both nuclear sequences and allozyme electromorphs for sets of populations of two currently recognized species of pocket gophers,Thomomys bottae andT. townsendii in the western United States. These molecular perspectives give somewhat conflicting views of polyphyly, paraphyly, and monophyly at the population and species level due, in part, to probable differences in times to monophyly, differential lineage sorting, retention of ancestral polymorphisms, and/or episodes of asymmetrical introgressive hybridization. As a consequence, strict adherence to any species concept in the objective recognition of evolutionary units within this complex is difficult at best.