The linear relationship between genetic distance and heterosis within maize heterotic groups has inspired efforts to predict heterosis using molecular markers in other species. In this study, three cytoplasmic male sterile and three restorer lines from a hybrid rice breeding program were crossed in all possible (9) combinations and the F1 offspring grown in replicated trials in three locations. Whole genome sequence analyses were used to identify hybrid pair genome-wide polymorphisms and the extent to which these polymorphisms were associated with heterosis estimated. The number of total hybrid pair SNP ranged from 150,823 to 331,876 and mid-parent heterosis from −13.6 % to 18.6 %. Hybrid pair total SNP, total INDEL, gene SNP and gene INDEL counts were generally correlated at the whole genome and chromosome level. There was a close correlation between chromosome SNP and INDEL frequencies while gene presence-absence analysis found little difference between cross combinations. The relationship between whole genome SNP and heterosis was best explained by a second order polynomial of negative sign, suggesting a positive heterotic response may be achieved by maintaining a balance between inbreeding and outbreeding depression, and that genome wide polymorphisms may have a role in predicting heterosis in rice.