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Flowering time is one of the most important traits in temperate fruit trees. Flowering time correlates with chilling requirements and ripening time. The mechanism controlling flowering time in these species could be conserved as suggested by the co-localization of QTL and the candidate genes for flowering time in several Prunus species. Currently, the molecular mechanisms underlying the regulation of flowering time remain poorly understood. In this study, three promising natural early-flowering/low-chilling-requirement mutants were identified and characterized: 'Rojo Pasion Precoz' and 'Bitlida Precoz' in apricot (Prunus armeniaca L.) and 'Santa Rosa Precoz' in Japanese plum (Prunus salicina L.). The advancement in flowering date with respect to the wild types was around one week in the case of 'Rojo Pasion Precoz' apricot cultivar, more than two weeks in 'Bulida Precoz' apricot cultivar, and between 9-27 days in the case of 'Santa Rosa Precoz' Japanese plum cultivar. In addition, they were fingerprinted using 44 SSR (Simple Sequence Repeats) and 21 SNPs (Single Nucleotide Polymorphism) markers. Fingerprinting analysis confirmed identical marker profiles between the wild types and their mutants. These results support the hypothesis that a somatic mutation or a stable epi-allele may underlay the early-flowering phenotype.