The genetic basis of three morphological traits (ovariole number, sternopleural bristle number and wing length) of Drosophila melanogaster has been investigated in natural populations that show great differences in these traits, i.e. Bordeaux (France) and Loua (Congo). F1 and F2 crosses, and chromosome substitutions between these two populations, were analysed. Maternal and/or X chromosome effects were found for sternopleural bristle number and wing length. For all traits, significant effects from each of the three chromosomes were found, but in general only one or two chromosomes had a major effect. Moreover, in all cases significant interactions between chromosomes were observed, suggesting the existence of epistatic effects. Our results are discussed and compared to those obtained from the analysis of selected laboratory strains.