Most studies of Hybrid Vigor (H.V) did not advance to the nature of the presence of homologous alleles controlling, as an effective force during hybridization and Heterosis. Current study indicated that the vigor and type of homologous alleles are responsible for the H.V, heterosis and purity, on the condition that alleles with a different hypothetical charge are compatible and are located on the same genetic loci, but when located on different genetic loci types that responsible for variation in F2. The segregation on the same genetic locus of the parental lineages will separate from each other decreases in F1. They are not distributed freely and H.V is not achieved, but the opposite occurs in inbred line with allelic compatibility that achieve high H.V. The homologous alleles are rearranged after pollination and fertilization, so H.V and heterosis appear. Found that the factors controlling of H.V are the type and H.V of compatibility of the action of locus, number of homologous alleles and genetic interactions affecting the action of the gene for that trait responsible for its inheritance. This explained the genetic purity of inbred, the reasons for its decreased, and clarified the complexities of the effect of genetic action and nature of the allelic pairs responsible for the inheritance of quantitative traits in F1. The genetic deterioration of hybrid vigor in F2. So the nature of charge and type of allelic compatibility of the genetic loci located on the gene could theoretically be an alternative or complementary to previous theories