Grain yield, agronomic traits, and correlation between genetic distance of 36 F₁ hybrids produced by half-diallel crosses using nine maize inbred lines were analyzed. In the analyses of F₁ hybrids and their mid-parent heterosis (MPH) for agronomic traits, grain yield showed highest MPH value of 156%. One-hundred kernel weight showed the lowest value of 7%. In addition, when genetic distance based on agronomic traits was estimated, parental inbred lines did not agree with their own pedigree. Therefore it had the limitation to estimate genetic distance using agronomic traits. In this study, 92 SSR markers were used to calculate genetic distance at DNA level. However we did not confirm their own pedigree of nine parental inbred lines. There was no correlation between grain yield and SSR markers. Therefore molecular marker selection was conducted in relation with grain yield by the step-by-step method using 92 SSR markers. The selected nine SSR markers showed a significant positive correlation (r²=0.703**) between grain yield and SSR markers. The correlations between the selected SSR markers and agronomic traits of ear length, ear width, plant height, and ear height were particularly showed positively correlated. The nine SSR markers selected in this study would help predicting heterosis and planning crosses for hybrids in maize breeding programs.

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