An economical detection method of simple sequence repeat with tailed primer M13(TP-M13-SSR) was used in genetic diversity analysis of 25 regional apple cultivars . The ranges of gene diversity, PIC and locus heterozygosity on 5 SSR loci were 0.5032～0.8448, 0.3952～0.8268 and 0.4400～0.9600，respectively. UPGMA cluster analysis showed that the apple species were classified into two groups, correlatively with geographic origin and relationship. The method has the advantages of high-throughput, sensitiveness, cost-effectiveness and high accuracy. And it had been used in studies on genetic diversity analysis of apple successfully. In addition, the merits and demerits of the TP-M13- SSR technique as well as the potential of application in analysis of genetic diversity in fruit tree were assessed.