This study was conducted at the farm of Sakha Agriculture Research Station during 2011 and 2012 growing seasons using nine parents and 36 hybrid combinations to study the relationship between genetic distances of parental genotypes and heterosis. The genetic distance of parental genotypes was determined by using functional genes markers related to yield traits. The correlation between genetic distance of parental genotypes and heterosis values was detected by determining 36 hybrids performance. The results indicated that the genetic distance was significant and positive correlated with grain yield/plant for mid-parent and standard heterosis estimates of r=0.46* and r=0.35*, respectively. While the parental genetic distance was not significant correlated with heterosis for some other traits among them: number of productive panicles/plant, 1000-grain weight, fertility percentage% and number of grains/panicle. Thus, the correlation coefficients was not sufficient enough among the parental genotypes for these traits and was not suitable to use molecular potentiality for heterosis prediction.