In order to differentiate species within the Borrelia burgdorferi sensu lato complex, LightCyler PCR and melting-curve analysis of the amplicons of two genes with intraspecies variability, the p66 gene and the recA gene, were performed. It was demonstrated that nested LightCycler PCR amplification of p66 is more sensitive in the detection of borrelia DNA than amplification of the recA gene. B. burgdorferi sensu stricto could be differentiated from Borrelia garinii and Borrelia afzelii by melting-curve analysis of the p66 gene amplicon. B. garinii could be differentiated from B. afzelii and B. burgdorferi sensu stricto by melting-curve analysis of the recA gene amplicon. Therefore, the PCRs complement each other in subtyping different Borrelia species, and combined LightCycler PCR and melting-curve analysis of both target genes is a rapid method to distinguish the three species of B. burgdorferi sensu lato.Lyme disease is the most prevalent tick-borne disease of the Northern Hemisphere (3). Its etiologic agent, Borrelia burgdorferi sensu lato, has been divided into different species. B. burgdorferi sensu stricto, Borrelia afzelii, and Borrelia garinii are the common human pathogenic species (4, 21). The infection leads to a variety of clinical symptoms involving the skin, nervous system, heart, and joints (19).Erythema migrans (EM) and acrodermatitis chronica atrophicans (ACA) represent common cutaneous manifestations of an infection by B. burgdorferi sensu lato (1, 13, 21), whereas the role of this spirochete in the pathogenesis of morphea and lichen sclerosus et atrophicus is controversial (13,15,23,25).Since PCR has proved to be a sensitive and fast method for the diagnosis of microrganisms which are difficult to culture, the technique has been applied to the detection of B. burgdorferi sensu lato DNA in infected ticks (6) as well as in human specimens, such as cerebrospinal fluid (4) or synovial fluid (5, 20), urine (2, 16), and skin (9, 24). Established PCR protocols amplify different segments of borrelial chromosomal genes, such as the flagellin gene (10, 15), the one-copy 16S rRNA gene (7), the 23S rRNA gene (17), the p66 gene segment encoding a 66-kDa protein (14), the recA gene (8), and the plasmid-encoded ospA gene (9,20).Common PCR with a conventional thermocycler and subsequent separation of the amplicon by agarose gel electrophoresis allows the detection of B. burgdorferi sensu lato DNA. Subtyping of Borrelia species DNA is not possible, since the intraspecies sequence polymorphisms of PCR amplicons are only a few base pairs long.Several postamplification methods were employed to identify Borrelia species commonly associated with Lyme borreliosis, e.g., oligonucleotide typing with PCR fragments (5), randomly amplified polymorphic DNA fingerprinting analysis (22), pulsed-field gel electrophoresis (4), single-strand conformation polymorphism (18), and subtype-specific PCR targeting the 16S rRNA gene (6). These techniques are usually time-consuming, and some of them require high technical standards and ...