Prunus serotina (black cherry) is native to America and has five subspecies: serotina, eximia, hirsuta, virens, and capuli. P. serotina subsp. capuli is found in Central and South America with superior fruits found in Ecuador. These have large, juicy, and tasty fruits used for human consumption. They are available in produce markets and have important nutraceutical properties. However, no commercial cultivars of capuli are currently available. The main goal of this research was to understand if different morphological characters can differentiate unique populations of P. serotina subsp. capuli present in Ecuador. Morphological traits (tree, leaf, and flower) of plants grown from the OP seeds of 44 capuli accessions collected from three provinces of Ecuador (Cotopaxi, Chimborazo, and Tungurahua) were characterized in 2019 and 2020. Tree measurements included the number of primary branches and growth habit. Leaf measurements included petiole length, leaf area, leaf height, leaf width, leaf apex angle, and leaf basal angle. Flower measurements included pedicel length, flower width, and flower length. Raceme length, number of racemes per branch, and number of flowers per raceme were also characterized. ANOVA were performed with significant differences observed among capuli accessions for all variables measured. No clear differences were observed across regions with PCA and cluster analysis that may support the presence of different populations.