Clark 63' and 'Harosoy 63' soybean (Glycine max (L.) Merr.) nuclei were each backcrossed into eleven cytoplasms of wild and ancestral soybean lines to produce twenty-two BC[subscript]5-derived near-isolines. The near-isolines were placed in five polymorphic groups based on the RFLP analyses of their chloroplast-DNA. The near-isolines were also placed in five polymorphic groups based on the RFLP analyses of their mitochondrial-DNA. Mean cp-RFLP and mt-RFLP performance were used to identify relationships between the cytoplasmic genomes and various traits. This study evaluated the days to reach growth stages, plant architectural traits, leaflet dimensions and dry weight, reproductive characters, protein and oil concentration of the seed, seed fatty acid and amino acid concentrations, photosynthetic rate, and leaflet nitrogen;Differences in the RFLP groups were found infrequently to be significant (Prob F < 0.05). However, several trends were observed in the performance of the RFLP groups having either the Clark or the Harosoy nuclei. The rankings for seed size and seed yield of the mt-RFLP groups having the Clark nucleus were identical to those of the mt-RFLP groups having the Harosoy nucleus. There was modest consistency across the nuclei in the ranking of the mt-RFLP groups in plant height and plant width at the time of beginning seed-fill. Trends were also found among the mt-RFLP groups in the concentrations of seed oleic, linoleic, and linolenic fatty acids;There was consistency in the seed yield of the cp-RFLP groups across the Clark and Harosoy nuclei. However, the trend was not as strong as that for the mt-RFLP groups. There was evidence to indicate that the cp-RFLP groups were associated with the CO[subscript]2-exchange rate. However, differences between the cp-RFLP group means were very small.