Crop wild relatives serve as an important genetic reservoir for their typically genetically depauperate domesticated counterparts. Unfortunately, crop wild relatives can be threatened by the fragmentation of human-dominated landscapes and crop-to-wild gene flow. The tropical fruit crop papaya (Carica papaya L.) grows naturally in the fragmented Mesoamerican landscape, sometimes alongside cultivated fields. We assessed the conservation risk to wild papaya populations using morphological and population genetic analyses of naturally occurring papaya in Panama, the southernmost extent of the papaya's natural geographic range. Wild papaya was typically small-fruited, with limited morphological variation among populations. Genetic diversity is reasonably high, though most populations exhibit moderate levels of bi-parental inbreeding. Gene flow was greatest between populations along the Panama Canal and the Pan-American Highway, though evidence of crop-to-wild gene flow was limited. While there is evidence of mild genetic erosion in wild papaya in Panama, genetic diversity is still moderately high, and gene flow exists across natural and artificial landscape corridors. Furthermore, abandonment of pastures may actually promote the population expansion of wild papaya into the fragmented landscape in its role as a pioneer species.