Yield and yield components in hybrid rice were investigated using AFLP, RAPD and SSR markers. Ten restorer and five male-sterile lines were crossed in all possible pairs resulting in 50 crosses. Positive loci, effect-increasing loci, effect-decreasing loci and non-environmental loci were selected from the 931 marker loci surveyed in the 15 parental lines and their correlation with yield and yield components were analyzed. The results indicated as follows (1) The correlation between genetic difference and yield and yield components calculated on all three molecular loci failed to reach significant level for most of the traits investigated and can not be used to predict yield and yield components directly. (2) Positive loci were of limited usefulness in the prediction of yield and yield components for their variation with different traits investigated despite that they can improve the correlation coefficient in some degree. (3) Effect-increasing and effect-decreasing loci can greatly improve correlation coefficient and may be used to predict the yield and yield components for their consistence with the environment. (4) The coefficient based on non-environmental loci was high though it was a bit lower than that based on effect-increasing and effect-decreasing loci. It indicated that environment had great effect on yield and yield components in rice.