We report the complete genome assembly of Yersinia pestis subsp. pestis bv. Medievalis SCPM-O-B-6530, a strain belonging to the most ancient phylogenetic group (group 2.MED0) of Y. pestis subsp. pestis bv. Medievalis. This proline-dependent strain, carrying an additional plasmid (pCKF), was isolated from the Central-Caucasian high-mountain plague focus in Kabardino-Balkar Republic, Russia.