In this study, we have identified the possible genetic factors responsible for fowl-adaptation of Salmonella entericaserovar Gallinarum (S. Gallinarum). By comparing the genes related to Salmonella pathogenicity islands (SPI) of S. Gallinarum with those of Salmonella entericaserovar Enteritidis (S. Enteritidis) we have identified twenty-four positively selected genes. Our results suggest that the genes encoding the structural components of SPI-2 encoded type three secretion apparatus (TTSS) and the effector proteins that are secreted via SPI-1 encoded TTSS have evolved under positive selection pressure in these serovars. We propose that these positively selected genes play important roles in conferring different host-specificities to S. Gallinarum and S. Enteritidis.