The genetic diversity and population structure of a Dalian (shihe) population of the wild Manila clam Ruditapes philippinarum with different ages were examined using SSR markers. The genetic diversity of the different ages (1 age, Age1; 2 age, Age2; and 3 age, Age3) was relatively high. Statistical analyses using POPGENE 1.31 and SPSS16.0 showed that the sites of Rp-11, Rp-12, and Rp-19, was well as the number of alleles significantly differed among the three ages (P < 0.01); the sites of Rp-20, Rp-24, Rp-27, and Rp-30 also significantly differed (P < 0.05); and the remaining seven sites had no significant difference (P > 0.05). The average number of alleles per locus was 4.3095, the effective number of alleles was 2.3729, and the polymorphic loci percentage P (%) was 14. The observed heterozygosity and expected heterozygosity were high; the average observed heterozygosity was 0.2335 and the average expected heterozygosity was 0.514. The changes in the Ne and He age followed the trend Age2 > Age3 > Age1. The observed and expected heterozygosity for each age were 0.2357, 0.2546, and 0.2159, as well as 0.4951, 0.5286, and 0.5184, respectively. The Age2 genetic diversity index was higher than Age1 and Age3, whereas genetic differentiation was relatively low among the three groups. Among them, the minimum Age1- and Age3-clam genetic distance was 0.0195, which was a small variation. In contrast, the genetic distance between Age1 and Age2 was 0.0437, indicating a small range (0.0195-0.0437). From a numerical point of view, there was great genetic similarity among the three ages of clams, with an average genetic identity of 0.9655. Age1 and Age3 have a genetic similarity of up to 0.9807, whereas the degree of similarity between Age1 and Age2 was small (0.9572). The clams with different ages had a very high degree of similarity. The calculated average genetic distances using the UPGMA clustering method revealed a smaller genetic distance between Age3 and Age1 clams than between Age3 and Age2 clams. Allele frequencies, calculated by the chi-square test, showed changes in the population structure with age, changes in parts of the gene, decreased allele frequency, and some alleles becoming fixed. The overall genetic differentiation was low, with an F_st values of 0.0248 (P < 0.05) for the Manila clam population of Dalian. The coefficient of gene differentiation in the different ages was 0.02, which showed that 2% of the total arose from differences among age groups. The genetic distance and genetic identity average between age classes were 0.035 and 0.9655, respectively. The mean gene flow (N_m=9.8238) was relatively smooth, and the age classes of genetic differentiation within a population of clams were less affected.