Fushiguang, Tengxi138, Shangyu397 and Wuyoudao1 are the founder parents of rice breeding at cold region from the 1990s. 50 SSR markers were used to cluster and PCO analyze the the founder parents and their derivatives. The results showed that 150 alleles were detected and allelic variation of single SSR loci ranged from 2-6, mean allelic variation was 3; PIC ranged from 0.0725-0.6845, mean 0.3655; 51 experiment varieties were separated into four classes and four founder parents were in four classes separately; four founder parents were far from each other and their derivatives distributed around them through PCO analysis. Only 3 in 39 rare alleles detected existed in founder parents. This showed that genetic improvement of cold rice has progressed to surround a few founder parents in recent years. Founder parents has transmitted their most fine genes to derivatives and pedigree analysis has the same result with SSR and PCO analysis.