Variation in the chromosomal genomes of 1527 isolates of eight common serotypes (O and H antigen profiles) of Salmonella was assessed by analysis of electrophoretically demonstrable allelic polymorphism at 23 metabolic enzyme loci. Seventy-one distinctive electrophoretic types, representing multilocus genotypes, were identified. A basically clonal population structure was indicated by the presence of strong linkage disequilibrium among enzyme loci, the association of each serotype with a relatively small number of multilocus enzyme genotypes, and the global distribution of certain genotypes. For each of six of the serotypes, 83-96% of isolates were members of a single clone. The occurrence of each of four serotypes (S. derby, S. enteritidis, S. infantis, and S. newport) in isolates of clones belonging to several evolutionary lineages, some of which are distantly related, suggests that the horizontal transfer and recombination of chromosomal genes mediating expression of cell-surface antigens has been a significant process in the evolution of the salmonellae. Two divergent clone clusters of S. derby differ in the relative frequency with which they cause disease in birds versus mammals, and two major lineages of S. newport differ in the frequency with which their clones are associated with disease in humans versus animals.