This study was carried out to analyze correlation between heterosis of F1 hybrids and the genetic distance of parental lines. Growth characteristics such as number of leaves, plant height, bulb diameter, bulb height, bolting rate and marketable yield were examined in 15 F1 hybrids. The genetic distance among one male sterile line and fifteen restorer lines were analyzed with SSR markers. 21 primer pairs amplified polymorphic band and the average number of polymorphic allele was 3.4. As a result of UPGMA cluster analysis, the similarity coefficient value among parental lines ranged from 0.43 to 0.63. Combination of M1 and R14 is high similarity and number of leaves, plant height and yield are 10.2, 66.7cm and 6,818kg·10a-1. The case of the lowest value combination, they are 9.0 and 63.7cm and 7,728kg·10a-1, respectively. The results showed that there are no significant correlations between genetic distance and heterosis of F1 hybrids and only molecular marker does not predict growth traits and yield of onion.