Abstract: Genetic diversity of 50 Prunus persica germplasms was analyzed using 16 pairs of SSR primers. The results showed that the polymorphism information contents of the individual sites ranged from 0.04 to 0.37 with an average of 0.24. The 50 peach germplasms could be classified into 3 groups according to thecluster analysis of the unweighted pair group method witharithmetic mean. They were medium late-maturing, medium early-maturing and low-temp early-maturing peaches. In addition, the low-temp germplasms with excellent over-all properties in the hot and humid southern regions could be grouped by themselves. The ornamental varieties were genetically far remote from the common peaches. A genetic analysis indicated that some of the local germplasms found in Fujian were typical southern peaches. Thus, from the molecular level, it confirmed the previous understanding of the origin of local varieties to be south of the Yangtze River.