The genus Persea consists of two subgenera, Persea (known as avocados) and Eriodaphne (known as aguacatillos, avocado-like species). The present study aimed to determine whether the genus Persea is a monophyletic group and whether the division into two subgenera is an artificial one. In conjunction with these goals, a hypothesis of the phylogenetic relationships among Persea species is proposed. Our results suggest that Persea is not a monophyletic group. Two clades of Persea can be recognized. The results suggest that Eriodaphne and Persea should be considered to be independent genera. Various leaf and floral characters contributed for separation into groups. The definition of Eriodaphne is based on fruit color, sessile glands at the base of the stamens, vein prominence and leaf shape. Persea is more closely related to genera Nectandra and Ocotea than Eriodaphne. The 11 species included in Persea are recognized as species. The group is defined by fruit flavor, mature leaf color, number of tertiary divergent veins, and pubescent bracts in the inflorescence. Within this group, a clade of six species in which P. guatemalensis is included is recovered by seed shape, venation pattern relief, and number of fruits per cluster. Moreover, the seed shape supports the separation of P. floccosa and P. zentmyerii. A molecular character analysis is necessary to support the Persea clades proposed herein. Nevertheless the phylogenetic relationships revealed by this study provide new bases for the selection and conservation of the species Persea.