Particular serovars of Salmonella enterica have emerged as significant food-borne pathogens in humans. At the chromosomal level, discrete regions in the Salmonella genome have been identified that are known to play important roles in the maintenance, survival, and virulence of S. enterica within the host. Interestingly, many of these loci appear to have been acquired by horizontal transfer of DNA among and between bacterial species. The profound importance of recombination in pathogen emergence is now just being realized, perhaps explaining the sudden interest in developing novel and facile ways for detecting horizontal transfer in bacteria. The Incongruence Length Difference (ILD) Test offers one such means. ILD uses phylogeny to trace sequences that may have been promiscuously acquired by exchange of DNA during chromosome evolution. We show here that the ILD test readily detects recombinations that have taken place in genes composing the inv-spa invasion complex (63 min) and the type 1 pilin complex (14 min) of S. enterica. Moreover, the mutS gene, whose product helps protect the bacterial genome from invasion by foreign DNA, appears to have undergone intragenic recombination within S. enterica subgroup I. This subgroup comprises the human pathogens, S. typhimurium and S. typhi. Our data affirm the application of the ILD test as one approach in identifying recombined sequences in the S. enterica chromosome. Furthermore, horizontally-acquired sequences within mutS support a model whereby evolutionarily important recombinants of S. enterica are rescued from strains carrying defective mutS alleles via horizontal transfer.