The positive correlation between level of heterozygosity and yield in autotetraploid alfalfa (Medicago sativa L.) suggests that genetic diversity between parents may be related to yield of their hybrid progeny. This was tested by comparing the levels of polymorphism among parental genotypes for restriction fragments homologous to 61 recombinant DNA clones with the yield of their single-cross progenies. Diploid (2x) genotypes were chromosome doubled to produce autotetraploids (4x), and these isogenic 2x and 4x genotypes were used as parents to generate progenies in 4 x 4 diallels. Seeds from reciprocal crosses were bulked to produce six single-cross families for field evaluation at each ploidy level. Yield data of single-crosses were collected in spaced-plant and microplot field trials over two and three years, respectively. Genetic dissimilarities (GDs) were estimated for all pairs of the four parents by the complement of the Dice coefficient calculated from 244 restriction fragments. At the diploid level, no significant associations between GD and yield of single-cross progenies were detected; however, high correlations were detected for tetraploid progenies in microplots and spaced-plant held trials (r = 0.69, p < 0.16 and r = 0.82, p < 0.05, respectively). Inconsistencies in correlations detected between GD and yields of isogenic 2x and 4x families may be related to the level of heterozygosity expected among progenies derived from heterozygous parents at different ploidy levels. Autotetraploids have more heterozygous loci due to tetrasomic segregation than equivalent diploids, and can benefit from greater complementary gene interactions. Although RFLP-based GD measurements do not appear to accurately predict yield of diploid single-cross progenies, results from this preliminary investigation suggest that molecular marker evaluation may be useful for predicting yield of tetraploid alfalfa hybrids.