Seed Coat Cracking (SCC) in soybean showing cracks in the surface of seed coat, causes serious effect on seed quality in soybean. However, breeding for resistance to SCC is difficult due to the complicated genetic behavior and environmental interaction. The objective of this research was to improve breeding efficiency for resistance to SCC based on DNA marker in soybean. In this study, SSR markers were used to identify the genomic regions significantly associated with the quantitative trait loci (QTL) that controls SCC in two segregating F_2:11 RIL populations, 'Keounolkong' / 'Shinpaldalkong' (K/S) and 'Keounolkong' / 'Iksan10' (K/I). The two populations were phenotyped at two locations in Suwon and Yeoncheon, Korea. In the K/S population, four QTLs for SCC were identified at Suwon, six at Yencheon, with total phenotypic variations of 6.68-12.18% and 3.65-11.69%, respectively. Two QTLs were commonly identified on the linkage group D1b and I at two locations, accounting for over 10% of the phenotypic variation. In the K/I population, three QTLs for SCC were identified at Suwon, four at Yeoncheon with total phenotypic variations of 5.26-8.45% and 3.26-11.23%, respectively. QTLs on D1b and D2 were commonly associated with SCC at two locations. Especially QTL tightly linked with Satt216 on LG D1b was commonly associated with SCC across populations and locations. Results showed that major QTL for SCC has been identified on LG D1b, D2, and I. And these major QTLs for SCC may be used for minimizing soybean SCC through effective marker-assisted selection (MAS).