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<p>Abstract</p> <p>Background</p> <p><it>Salmonella paratyphi </it>C, like <it>S. typhi</it>, is adapted to humans and causes typhoid fever. Previously we reported different genome structures between two strains of <it>S. paratyphi </it>C, which suggests that <it>S. paratyphi </it>C might have a plastic genome (large DNA segments being organized in different orders or orientations on the genome). As many but not all host-adapted <it>Salmonella </it>pathogens have large genomic insertions as well as the supposedly resultant genomic rearrangements, bacterial genome plasticity presents an extraordinary evolutionary phenomenon. Events contributing to genomic plasticity, especially large insertions, may be associated with the formation of particular <it>Salmonella </it>pathogens.</p> <p>Results</p> <p>We constructed a high resolution genome map in <it>S. paratyphi </it>C strain RKS4594 and located four insertions totaling 176 kb (including the 90 kb SPI7) and seven deletions totaling 165 kb relative to <it>S. typhimurium </it>LT2. Two rearrangements were revealed, including an inversion of 1602 kb covering the <it>ter </it>region and the translocation of the 43 kb I-CeuI F fragment. The 23 wild type strains analyzed in this study exhibited diverse genome structures, mostly as a result of recombination between <it>rrn </it>genes. In at least two cases, the rearrangements involved recombination between genomic sites other than the <it>rrn </it>genes, possibly homologous genes in prophages. Two strains had a 20 kb deletion between <it>rrlA </it>and <it>rrlB</it>, which is a highly conservative region and no deletion has been reported in this region in any other <it>Salmonella </it>lineages.</p> <p>Conclusion</p> <p><it>S. paratyphi </it>C has diverse genome structures among different isolates, possibly as a result of large genomic insertions, e.g., SPI7. Although the <it>Salmonella </it>typhoid agents may not be more closely related among them than each of them to other <it>Salmonella </it>lineages, they may have evolved in similar ways, i.e., acquiring typhoid-associated genes followed by genome structure rearrangements. Comparison of multiple <it>Salmonella </it>typhoid agents at both single sequenced genome and population levels will facilitate the studies on the evolutionary process of typhoid pathogenesis, especially the identification of typhoid-associated genes.</p>