The genus Genipa is a widespread, lowland, Neotropical lineage of trees in the coffee family, Rubiaceae. There is long-standing disagreement on the delimitation of species in the genus and how broadly Genipa is circumscribed. Here, we use genomic data to resolve the classification within Genipa. Using target sequence capture we generated a high-resolution 245-locus dataset to produce a comprehensive species phylogeny under the multi-species coalescent model. The phylogenomic results strongly support Genipa spruceana, often synonymised with Genipa americana, as a distinct monophyletic species. Similarly, the monophyly of Genipa infundibuliformis, a recently recognized species, is also strongly supported. The phylogeny also shows three distinct, well-supported clades within the widespread species, Genipa americana. These clades are interpreted as three independently evolving lineages in contrast to the two varieties most commonly recognized in G. americana based on previous morphological studies.