Black stem disease is one of the most important fungi diseases in sunflower. Information about the mode of heritability and the effects of genes controlling trait could be most important for selecting breeding methods to black stem disease resistance. In this study, genotypes ENSAT-B5 and AS613 and a mutant genotype M5-54-1 with different response to MP8 and MP10 isolates were selected and F1, F2, BC1 and BC2 generations were made from ENSAT-B5×AS613 and ENSAT-B5×M5-54-1 crosses. Generations of crossing and parents of each set were planted in a completely randomized design with three replications and infected by M8 and M10 isolates. With the exception of the [(♀) M5-54-1 × ENSAT-B5 (♂)-MP10] cross, the lack of fit test of simple three parametric additive-dominance models for the [(♀) AS613 × ENSAT-B5 (♂)-MP8] and [(♀) AS613 × ENSAT-B5 (♂)-MP10] crosses were significant, indicating the presence of non-allelic interactions in the inheritance of the black stem disease resistance. In the estimated models for the different crosses, high and significant amount of dominant effects and dominant × dominant interactions suggested the importance of non-additive genetic effects. Therefore, selection for this trait in early generation could not be effectively successful and hybrid development is highly recommended for increasing the resistance to the black stem disease.