The genus Prunus (Rosaceae) includes economically important species such as peaches, plums, almonds, and cherries. Past phylogenetic studies identified three major clades within the genus corresponding to inflorescence types: corymbose, solitary, and racemose. The corymbose and solitary groups are found in temperate regions, whereas the racemose group occurs in temperate, neotropical, and paleotropical regions. These previous phylogenetic studies reported discordance between nuclear and chloroplast phylogenies. In chloroplast phylogenies, the racemose group was invariably monophyletic, whereas the relationships among the major lineages in nuclear phylogenies were unclear. Phylogenetic uncertainty has clouded biogeographic reconstructions, although the origin of Prunus is hypothesized to be in eastern Asia, with several tropical to temperate transitions allowing it to spread to its current range. In this study, morphological, environmental, and genetic data were used to examine how these transitions occurred. Environmental conditions were examined using principal component analyses of bioclimatic variables, morphology was analyzed using machine learning algorithms applied to digitized herbarium sheet image data, and phylogenetic analyses were conducted based on 610 nuclear loci and complete chloroplast genomes generated via HybSeq. Our nuclear phylogeny supports that the temperate racemose species form a clade with the solitary and corymbose lineages, which are then sister to the tropical racemose group. Machine learning classification of herbarium images inferred that most of the temperate species were more similar morphologically to paleotropical species as opposed to neotropical species. This result, in combination with the environmental space occupied by each major lineage within the genus, suggests that the temperate species' morphological similarity to neotropical species did not arise due to shared environmental conditions. Further investigation of individual species such as Prunus serotina, reveals the morphological, genetic, and environmental variation found throughout their large North American range, informing our understanding of the temperate to tropical transitions. This work improves our understanding of the biogeographic transitions from tropical to temperate regions throughout the evolutionary history of the genus Prunus, and illustrates how morphological and environmental data can be used to supplement our phylogenetic research.