AbstractConservation of maize inbred lines in different stations causes variability among strains. The objective of this research was to determine agronomic and molecular differences in American sweet corn inbreds maintained in Spain. American and Spanish strains of five sweet corn inbred lines were characterized by using 34 RAPD primers that produced 168 consistent bands. Strains of four of these inbreds were crossed in a diallel design, and hybrids were evaluated in four environments in northwestern Spain. The RAPD characterization showed no differences between strains for two inbreds, while divergence between strains was largest for the inbred 15125. Most primers did not reveal any variability between pairs of strains, while some primers produced variations at high rates. Differences in agronomic performance among Spanish and American strains were most important for P51, followed by P39, while strains 1453 or 15125 were not significantly different. Molecular differences between strains were not related to agronomic performance. Residual heterozygosity or outcrossing cannot explain these results. Lack of adaptation could have caused stress‐induced mutagenesis. Natural selection could have eliminated unfavourable selective mutations, but neutral mutations can be found at the molecular level and favourable mutations could have been selected at the agronomic level.