Heterotic performance of hybrids is dependent upon the amount of genetic variability among parents and combining ability of alleles at the loci associated with target traits. This study was carried out to determine if (1) pedigree-based genetic distance could explain molecular levels of genetic diversity, and (2) molecular marker-based genetic distance could predict the degree of hybrid performance in barley. The average value of Random Amplified Polymorphic DNA (RAPD)-based genetic similarity for all 58 genotypes was 0.641. Twenty-two hulless barley and eight malt barley varieties showed low levels of genetic diversity with higher similarity values than the average of all or of the hulled barley variety pool. Coefficients of parentage (COPs) computed for 1,653 pairs of 58 Korean barley varieties ranged from 0 to 0.984 with a mean of 0.048. Correlation between the genealogical and RAPD-based genetic similarity matrices was 0.256 (P < 0.01). Correlation values for the related and for all (related + unrelated) genotype pairs were almost similar to each other, indicating that the unrelated genotypes share a large portion of genomes alike in state, not identical by descent. RAPD-based genetic similarity estimates among parents were poorly correlated with their hybrid performance such as 1,000-grain weight (r = 0.34), biomass yield (r = -0.12), and grain yield (r = -0.04) for 11 genotype pairs of hulled barley. However, correlations between heterozygosity at marker loci and hybrid performance for biomass and grain yield slightly increased when two F1 hybrids were excluded in the analysis due to their low yield.