Alterations to the Pecos River in New Mexico and Texas, USA, including damming and river channelization, plus water extraction and diversion from, and pollution of associated habitats during the 19^th and 20^th centuries have greatly impacted many fish species. The Pecos pupfish (Cyprinodon pecosensis) is one species that was heavily impacted, especially because introduction of a congener, the sheepshead minnow (C. variegatus), to the Pecos River in the 1980s eliminated pure C. pecosensis from most of its range via hybridization. Currently, C. pecosensis is restricted to generally small isolated habitats, although historically this species had a large metapopulation with a large geographic range. The current study was an initial survey of morphological variation within different isolated habitat complexes to determine if there were habitat-morphotype distinctions. We used analysis of convex hull coverage (ACHC) with geometric morphometric data to assess whether morphotypes were distinct. ACHC results confirmed that three morphotypes were evident in the Bitter Lake National Wildlife Refuge: deep sinkhole, riverine, and marshland morphotypes. Alternatively, connectivity between a deep sinkhole and marshland habitat in the Bottomless Lakes State Park appeared to produce non-extreme body shapes with little variation, suggesting gene flow mitigates morphological divergence. Results from this study highlight that disruption of gene flow in metapopulations can spur divergent evolutionary trajectories in isolated populations. For species with conservation concern, like C. pecosensis, it is not clear if re-establishing gene flow would be beneficial or detrimental for populations that are potentially adapted to their local environments.