This article considers the molecular genetic and ecological approaches to solving the problem of the origin of the plague-causative agent microbe Yersinia pestis. The initial conditions of the conversion of the clone of saprozoobiont pseudotuberculosis microbe Yersinia pseudotuberculosis O:1b to the population of plague microbe Yersinia pestis are described. It is shown that a remote biogeocenotic precondition for speciation was the aridization of Central Asian landscapes, which resulted in the formation of the species-specific behavior of the Mongolian tarbagan marmot (Marmota sibirica): the arrangement of plugs in wintering burrows with the use of their own excrement. The last maximal Sartan cooling, which covered the areas of Central Asia 22000–15000 years ago, became a recent biogeocenotic precondition that served as a direct inducer of the speciation process. The deep freezing of the ground caused a shift in the behavior of one of the components of biocenosis, namely, the larvae of the marmot flea Oropsylla silantiewi: they began to change from saprophagy to hematophagy in winter months. This phenomenon led to the direct (traumatic) contact of excrement with blood in the oral cavity of marmots during hibernation. The traumatic penetration of pseudotuberculosis microbe into the blood of Mongolian marmots for the whole population during hibernation created conditions for the implementation of stable bacteremia and the development of the original epizootic M. sibirica–O. silantiewi–Y. pestis plague system. The psychrophilic properties and virulence are considered necessary preadaptive properties for pseudotuberculosis microbe to invade the host–parasite (rodent–flea) environment.