Salmonellae are enterobacteria responsible for outbreaks of human and animal clinical diseases, with important hygienic and economic consequences. Accurate epidemiological studies require the use of efficient markers, which make it possible to trace the establishment and diffusion of different bacterial strains and also to evaluate the similarities between different isolates. Numerous phenotypic and genotypic markers applicable to Salmonella are available for these epidemiological studies. Nevertheless, the relative interest of those markers depends on the serotypes, and a different hierarchy can be achieved for the Typhimurium and Enteritidis serotypes.