To know the relationships between phenotypic and genetic variables in a germplasm collection of fruit crops is useful a pre-breeding and cultivar distinctness. A core collection of 23 peaches/nectarines (Prunus persica (L.) Batsch), and 16 Japanese plum (Prunus salicina Lindl. var. salicina) cultivars were evaluated for 33 and 29 characteristics (botanical/ productive) respectively during two growing seasons. Also, eight specific simple sequence repeats (SSRs) markers were analyzed in both species. Principal components analyses revealed seven characteristics (related to the size of the fruit and the firmness of the pulp) as the most important for the 23 peach/nectarine cultivars and four characteristics (yield, fruit size, soluble solids, and harvest time) for the 16 Japanese plum cultivars. These analyses revealed three cultivars of peaches (Diamond Princess, Dixon, and Dr. Davis) and three of nectarines (Ruby diamond, Artic sweet, Summer fire) with the highest values for fruit size and pulp firmness. Four Japanese plum cultivars (Angeleno, Flavor Rich, Red Heart, and Pink Delight) showed the highest values of yield, fruit size, soluble solids, and harvest time. Elite germplasms to carry out a breeding program were identified from both the phenotypic and genetic analysis. Additionally, cultivar-specific SSR alleles were identified and are a relevant tool for cultivar distinctness.