The evolution of new genes, adaptation to environmental stresses and resistance to chemotherapies commonly occur through reorganization or doubling of large DNA regions to generate gene duplications. Further amplifications can arise if such rearrangements confer greater fitness benefits to the individual. Formation of gene duplications is highly conserved across many species, resulting from DNA repair of endogenous and exogenous DNA damage. Salmonella enterica serovar Typhimurium LT2 was used to study gene duplications because it has a short generation time, well-studied genome and genetic system easily amendable to manipulations. In addition, the laboratory Salmonella LT2 strain retains four active prophages (Gifsy-1, Gifsy-2, Fels-1 and Fels-2), similar to infectious Salmonella; in contrast to laboratory strains of E. coli, which have only fragments of defective phages. Our study examined the contribution of these prophages on gene duplication formation by comparing lysogenic LT2 strains to LT2 strains lacking these prophages. We also compared derivatives of these parental strains with genetic defects in genes required for several major DNA recombination pathways. To do so, we used a DNA binding protein, ParB, fused to Green Fluorescent Protein (GFP). ParB binds to a specific DNA sequence, parS, inserted in the chromosome between two homologous ribosomal RNA genes. We assessed the frequency of gene duplications based on variations in focus intensity and the number of foci within a cell. Quantitative PCR and classical transduction experiments were implemented as additional ways to determine gene duplications. We find that in recA and ruvC mutant strains prophage presence facilitates the formation of gene duplications.