Main features of mutagenesis induced in the double super-unstable system in Drosophila melanogaster males and females was studied earlier. Very different y- and sc-alleles arose under the mutagenesis. These are differed one from another by the expression of yellow and scute loci. However, it was shown that the female's mutagenesis very differed from the male's one. The structure of a homologous chromosome has played an important role in the mutagenesis in Drosophila females. We found here that the homologous translocation in Y chromosome led to double decrease of the frequency of the mutagenesis in males. It is proposed that interconnections between two homologous insertions are essential in the recombinational processes by which alleles change. The nature and mechanism of the sub-lethal allele's formation in the presence of translocation in Y chromosome is discussed.