Japanese apricot (Prunus mume) cultivars have been classified into several subpopulations, such as fruiting, fruiting-small, and ornamental, based on a variety of morphological traits and human preference. A recent genome-wide analysis indicated that these subpopulations show some genetic differentiation, but the fruit traits remain to be investigated. Therefore, we investigated phenotypic diversity of several fruit traits, such as sugar, organic acid, and volatile compound contents and compositions, in a variety of cultivars of Japanese apricot (P. mume), apricot (P. armeniaca) and their interspecific hybrids. We found that Japanese apricot cultivars show diverse phenotypic variation and that some fruit traits appeared to be associated with the differing subpopulations. The fruiting cultivars investigated appear to have higher contents of sugars and favorable volatile compounds such as lactones and esters. We also found that ‘Joshuhaku’, a local cultivar in Kyoto Prefecture, has desirable fruit traits including large fruit size, high contents of organic acid and favorable volatile compounds. Moreover, interspecific hybridization was found to have large effects on fruit traits. Our results indicated a wide diversity of fruit traits in Japanese apricot, in which sugars and volatile compounds were associated with fruiting cultivars. These observations may assist with the breeding of new Japanese apricot cultivars.