Treponema pallidum includes three subspecies of antigenically highly related treponemes. These organisms cause clinically distinct diseases and cannot be distinguished by any existing test. In this report, genetic signatures are identified in two tpr genes which, in combination with the previously published signature in the 5′ flanking region of the tpp15 gene, can differentiate the T. pallidum subspecies, as well as a simian treponeme. Copyright © 2006, American Society for Microbiology. All Rights Reserved.