In the presented work, six Borrelia burgdorferi sensu lato isolates were recovered from Ixodes ricinus ticks and one strain of spirochete with uncertain taxonomic position isolated from Culex pipiens mosquito collected in the Valtice area (South Moravia, Czech Republic), as well as representative type strains, were further characterized by ribotyping and whole-cell protein fingerprinting. The ribotype patterns obtained with HindIII and EcoRV ribotype patterns showed good correlations with the recently proposed genotypes and grouped each genospecies in a well-separated cluster. The whole-cell protein profiles of genospecies were more heterogenous than the ribotype patterns. The non-identified spirochetal strain was clearly separated from the Borrelia isolates in both methods thus proving their good capacity to characterize Borrelia burgdorferi sensu lato strains.