SEPALLATA (SEP) MADS box genes play essential and diverse roles in reproductive organ development. To investigate the SEP gene function in peach we isolated three SEP-like genes, PrpMADS2, PrpMADS5, and PrpMADS7, which belong to distinct SEP gene clades. They appeared as single copy genes in the peach genome and were found to preferentially express in flowers and fruits. Arabidopsis transformants expressing 35S: PrpMADS2 were indistinguishable from wild-type plants. Overexpression of PrpMADS5 led to earlier flowering. Through chimeric repressor silencing technology, PrpMADS5 was found to function in floral organ development. Expression of PrpMADS7 in Arabidopsis caused a dramatic attenuation of both juvenile and adult growth phases and, in severely affected plants, it led to flower formation immediately after the embryonic phase. Two microsatellite markers were developed for PrpMADS2 and PrpMADS5 and assigned to the genetic linkage groups 5 and 1, respectively. PrpMADS7, previously identified as PrpAGL2, and PrpMADS5 were identified as potential loci to modify the flowering time and floral organs in Prunus species. Moreover, our results showed the diversification of SEP genes in peach.