Identifying marker loci related to combining ability (CA) for yield trait in parents of japonica hybrid rice facilitates improving CA of parents and enhancing standard heterosis degree of japonica rice by using molecular marker-assisted selection techniques. F1 seeds of 90 combinations were made by hand-crossed nine CMS lines with ten restorer lines using North Carolina Design II. The F1 populations were planted in Nanjing and Xuyi environments, and six yield traits were investigated. CA of the 19 parental lines was analyzed for six yield traits respectively using the data of 90 F1’s. Combining the data of CA and SSR marker genotypes of the 19 parental lines, SSR marker loci related to CA for six yield traits were detected. Results showed that BT-18A and Wuqiang A were elite CMS lines, and C418 was elite restorer lines in both environments. Number of detected SSR marker loci related to CA for effective panicles per plant, spikelets per panicle, filled grains per panicle, seed setting rate, 1000-grain weight and daily yield per plant were 8, 13, 11, 6, 6, and 2, respectively in Nanjing, 12, 21, 8, 15, 10, and 7, respectively in Xuyi, and 4, 11, 5, 3, 5, and 1, respectively in both environments. Heterozygous genotype marker loci showing positive heterosis accounted for 74% (34/46) in Nanjing, and 53% (39/73) in Xuyi. Among the SSR marker loci detected in both environments, three were each co-associated with CA for three yield traits, and another three for two yield traits. The remaining 14 marker loci were each associated with CA for one yield trait. Through data-base searching, genes/QTLs for the corresponding traits were found nearly ten of the marker loci detected in both environments. Strategies of enhancing CA for yield traits of restorer lines in japonica rice using the marker loci identified in this study were discussed.