<h3>Introduction</h3> Outer membrane proteins (OMPs) play critical roles in disease pathogenesis and are vaccinogens. Topologic characterisation of surface-exposed β-barrels of <i>Treponema pallidum</i> (<i>Tp</i>) Nichols rare OMPs enabled a novel strategy to assess sequence diversity and evolution of <i>Tp</i> in geographically diverse locations. <h3>Methods</h3> Through early 2017, sequences encoding TprC (TP0117), TprD (TP0131), and BamA (TP0326) β-barrels were amplified from secondary syphilis patients from Cali (n=16) and swabs from patients in San Francisco (SF, n=6) and Czech Republic (CZ, n=9). Strains were assigned to the Nichols or SS14 clade based on <i>tp0548</i> and/or <i>tp0558</i> sequences. <h3>Results</h3> 23 assignable CZ and Cali strains belonged to either the SS14 or Nichols clade (SS14 predominant), while all 6 SF strains belong to the SS14 clade. Sequence diversity at the three OMP loci was greatest in Cali, with evidence of recombination within <i>tprC</i> and <i>bamA</i> alleles, as well as between strains and clades at all 3 genetic loci. SF strains contained nearly identical sequences at all 3 genetic loci. The SS14 and Mexico A reference strains, both belonging to the SS14 clade, have identical <i>tprDs</i> (<i>tprD2</i>) but different <i>tprC</i> and <i>bamA</i> alleles. Mexico A <i>tprC</i>s were common at all three geographic locations, including Nichols clade strains from Cali. Mexico A <i>bamA</i>s were prevalent in Cali and SF, while CZ SS14 clades contained only SS14 <i>bamA</i>s. OMP sequences were obtained from all three loci in 7 of 8 Nichols clade strains. Of these 7, only 1 matched the Nichols reference strain, while the other 6 contained Mexico A alleles in at least 1 OMP locus. Of the 21 SS14 clade strains, 10 contained Mexico A alleles at all 3 loci; 2 contained Mexico A <i>trpCs</i> and Nichols <i>bamAs</i>; and 9 contained Mexico A <i>tprCs</i> and SS14 <i>bamAs</i>. <h3>Conclusion</h3> OMP loci are evolving independently within <i>Tp</i>. Recombination of OMP sequences appears to be occurring between <i>Tp</i> strains and clades within patients. Mexico A OMP alleles are circulating widely among <i>Tp</i> strains. These findings have major ramifications for syphilis vaccine development.