Estimates of genetic diversity based on molecular and morphological data are common in the literature; however, they do not take the most agronomically important traits into consideration. Use of these estimates for recommending parent lines has not had much practical success because the populations thus generated generally exhibit wide variability, but medium to low means for the target trait. A total of 17 common bean cultivars were evaluated in 31 trials conducted in 2008, 2009, and 2010 in the rainy, dry, and winter crop seasons in Brazil. Twelve traits of agronomic importance were evaluated. Analysis of variance were performed on the data and the means were used to estimate the Euclidean distances. In addition, leaves were collected, DNA extracted, and amplification reactions were performed with 33 microsatellite markers to obtain the genetic distances based on complement of the weighted similarity indexes. The genotypes were clustered by the Tocher method. Both forms of estimation of genetic distance showed diversity among the cultivars. The Pearson correlation estimate between the agronomic and molecular genetic distance matrices was significant (0.32), but of low magnitude, which indicates that the distances estimated by the two sets of data supply different information. Coincidence between the clusters was 53%, confirming that this information can truly be considered complementary. The phenotypic mean values for grain yield, the divergence estimates, and the clusters formed by phenotypic and molecular data indicated some crosses with greater probability of obtaining higher yielding lines: BRSMG Majestoso × CNFC 10431, BRS Estilo × BRS Notável, and BRS Estilo × BRS Pontal.