Yield is the most important and complex trait for genetic improvement in crops, and marker-assisted selection enhances the improvement efficiency. We phenotyped 203 O. sativa accessions for 14 agronomic traits and identified five highly and significantly correlated with grain yield per plant. Genotyping with 155 genome-wide molecular marker demonstrated five main cluster groups Linkage disequilibrium (LD) decayed at least 20 cM and marker pairs with significant LD ranged from 4.64 to 6.06% in four main groups. Thirty marker-trait associations were highly significant, four for yield itself and three for plant height, six for plant weight, nine for tillers, five for panicle length and three for kernels/branch that were correlated with yield. Twenty-one markers contributed to the 30 associations because eight were co-associated with two or more traits. Allelic analysis of OSR13, RM471 and RM7003 for their co-associations with yield traits demonstrated that allele 126bp of RM471 and 108bp of RM7003 should receive greater attention because they had the greatest positive effect on yield traits. Tagging the QTLs responsible for multiple yield traits may simultaneously help dissect the complex yield traits and elevate the efficiency to improve grain yield using marker-assisted selection in rice.