ABSTRACTWe report sequences of the complete linear chromosome and five linear plasmids of the relapsing fever spirochete “CandidatusBorrelia fainii” Qtaro. The chromosome sequence of 951,861 bp and the 243,291 bp of plasmid sequences were predicted to contain 852 and 239 protein-coding genes, respectively. The predicted total GC content was 28.4%.