Reliable taxonomic relationships can provide a solid basis for deducing relationships and evolutionary history. Yet, when I began working with Y. pestis in 1998, the relationships between Y. pestis and Yersinia pseudotuberculosis were not obvious from the general literature, nor was it clear which of these closely related organisms was more ancient (Brossollet and Mollaret, 1994). 25 years ago, DNA-DNA hybridizations between multiple isolates of Y. pestis or Y. pseudotuberculosis and 3 labelled DNA preparation from either Y. pestis or Y. pseudotuberculosis were unable to distinguish between the bacteria from these two “species” (Bercovier et al., 1980). These analyses included 13 Y. pestis isolates of the biovars Orientalis, Medievalis and Antiqua, but did not include pestoides isolates (see below). Although Bercovier et al. recommended that taxonomists refer to both Y. pestis and Y. pseudotuberculosis as subspecies of Y. pseudotuberculosis (Bercovier et al., 1980), this recommendation has met with little or no compliance, possibly because scientists working with Y. pestis are so focussed on its pathogenicity, which is not properly a taxonomic criterion. (For similar reasons, a unique genus designation, Shigella, continues to be used for some Escherichia coli that cause epidemic dysentery (Lan and Reeves, 2002)). This situation may be convenient for medically oriented scientists, but can be very confusing for population geneticists.