Although syphilis and yaws have different clinical manifestation, the pathogens are microscopically and serologically indistinguishable. Genome scale approaches (microarray hybridisations and whole genome fingerprinting, WGF) showed that there are no gene deletions and multiplications and no large indels. Relatively subtle genetic differences responsible for different pathogenesis of syphilis and yaws thus require complete genome sequence of TPE. Physical map of complete genome sequence obtained by combination of CGS and DDT of heterologous regions was confirmed by WGF. CGS together with DDT sequencing and WGF was employed to obtain complete genome sequence of TPE Samoa D strain. The unfinished complete genome sequence comprised 1 linear contig. In silico proteome analysis revealed that more than 300 proteins (out of 1039 proteins predicted in TPA Nichols strain) were affected by sequence changes. The genome sequence of yaws treponeme was used to define intersubspecies difference between TPE and TPA.