Domesticated tree species represent an economically and ecologically important group of taxa. Trees differ from other well-studied crop systems (rice, wheat, corn, sunflower) in several basic biological attributes, all of which influence the way in which genetic variation is structured in these organisms. The goals of this study were to delimit a lineage of a Mesoamerican domesticated tree, Spondias purpurea, and to investigate the relationship between this lineage and another sympatric congener (S. mombin) using nuclear and chloroplast sequence data. The fourth intron of Pepc was sequenced for sixty-eight Central American Spondias trees including twelve S. mombin accessions, 55 S. purpurea trees, and one S. radlkoferi individual. Data were analyzed using traditional phylogenetic techniques and using a network approach. Nuclear data were compared with previously published sequence data from the chloroplast spacer trnS-trnG, revealing that the Spondias purpurea lineage includes both cultivated and wild populations, but in localized areas hybridization and incomplete lineage sorting blur the boundaries between the crop species and a sympatric congener. This study provides insight into the nature of a domesticated tree lineage, which, in the case of Spondias purpurea, is generally distinct despite some evidence for ongoing gene flow.