AFLP markers resolve intra-specific relationships and infer genetic structure among lineages of the canyon treefrog, Hyla arenicolor

► We use AFLP data to resolve intra-specific relationships in the canyon treefrog. ► Placement of a divergent Balsas Lineage is congruent with behavior and morphology. ► Most mtDNA Lineages also show high divergence in the AFLP data set. ► Some lineage relationships have improved resolution. ► Introgression and hybridization strongly influenced the history of this species.