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Borrelia valaisiana is a recently described bacterial species in the Borrelia burgdorferi sensu lato complex. To further characterize this bacterium, the plasmid-encoded ospA genes from eight B. valaisiana isolates were amplified by PCR, cloned and sequenced. All B. valaisiana isolates studied possessed an ospA gene with a size of 822-825 bp. The identity of the predicted amino acid sequences of the OspA proteins among B. valaisiana isolates was 69.1-100%, and ranged from 68.2 to 79.1% between B. valaisiana and other B. burgdorferi sensu lato species. Based on the OspA protein sequences, the eight B. valaisiana isolates could be distinguished into two subgroups. Subgroup I contained six B. valaisiana isolates of which OspA sequences were almost identical, but clearly differed from other LB spirochetes. Subgroup II consisted of two isolates with identical OspA sequences which were only 70% identical to subgroup I B. valaisiana isolates and similarly distant from the OspA sequences of other B. burgdorferi sensu lato genospecies. Phylogenetic analysis indicates that B. valaisiana isolates belonging to subgroups I and II possibly evolved from two distinct ancestors. Our data showed for the first time a major difference in OspA proteins within a well-defined B. burgdorferi sensu lato species at the evolutionary level, suggesting that it is not always reliable to assign Borrelia isolates to a definite species solely based on data from ospA gene sequence analysis.