Ten species are up to now recognized among Borrelia burgdorferi sensu lato complex. Among those, only three (Borrelia burgdorferi sensu stricto, B. garinii and B. afzelii) are reported to be pathogenic for humans and each responsible for a predominant clinical form of Lyme borreliosis. Each species is characterized by its vectors (Ixodidae), its host spectrum, its organotropism (for the pathogenic ones) and its geographical repartition. Borrelia are strictly parasitic and essentially clonal bacteria. Our goal was to explore the diversity of this bacterial complex. We selected, by several molecular markers, atypical isolates and compared them to already known species representative strains by RFLP or sequencing. The results show an unexpected diversity at a level which could be a species one leading to the conclusion that the structure of the Borrelia burgdorferi sensu lato complex is a high number of small (by their populations) clones among which emerge some large ones usually corresponding to the pathogenic species. Our data also allow to speculate on when, where and how these species evolved and migrated.