The bloody clam, Tegillarca granosa, is an important commercial bivalve which is extensively cultured from South Korea to Malaysia. Due to its economic value, it is important to cultivate rapid growth strains for the sustainable development of aquaculture industry of T. granosa. The emergence of molecular markers provides a rich theoretical basis for the rapid cultivation varieties. By the method of group selection, the rapid growth strains of T. granosa were bred though two generations. According to the comparison test, the rapid growth strains showed significant advantages in shell length, shell height, shell width and total weight than control group under the same environmental conditions. AFLP marker was applied in this study to evaluate the genetic variation of the rapid growth strains, and to screen the molecular markers associated with the traits of growth. A total of 2180 bands were amplified from 64 individuals of the rapid growth strain and control group by 40 primer combinations. The analysis of Nei’s genetic diversity index and Shannon’s genetic information index of two groups indicated that the genetic diversity of breeding group was slightly higher than the control group. The genetic distance between two groups was about 0.011 3, the value of GST was 0.022 4 and Nm was 22.281 1, from which we concluded that there is a little genetic differentiation after selection. Of all amplified bands, 7 bands showed significant differences in frequency between two groups. 2 bands of all were only found in rapid growth strains, with the frequency of 0.812 5 and 0.343 8, respectively. And 2 bands showed significantly higher frequencies in rapid growth strains, while 3 bands showed significantly higher frequencies in control group. The bands with higher frequencies in rapid growth strains may be associated with the traits of growth. The unique AFLP markers associated with growth traits would be useful for growth-related gene cloning, quantitative trait locus (QTL) mapping, and molecular-assisted selection (MAS) of T. granosa.