Phomopsis seed decay (PSD) is part of a major fungal disease complex found in most soybean production areas of the world. To establish the genetic linkage map and efficient soybean breeding program, DNA markers were surveyed for polymorphism between PSD resistant (cv. PI 417479) and susceptible (cv. Hwaeomput-kong) varieties. F2, BC1F2, BC2F2 and the corresponding F2:3 population families were used to evaluate the correlation between molecular markers and resistance to PSD. In SSR analysis, Sct_033 was the most significantly associated with PSD resistance among selected eight primers. AF1, AF2, and AF3 were also selected in AFLP analysis. And a few promising lines could be selected from two times of back cross. Especially a breeding line SS01415-8-1 was developed, which has high seed quality such a large seed size, bright hilum color, round shape, and etc. It might be considered a good breeding material for new recommend variety having resistance gene to PSD with good seed quality.