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We conducted genomic population and phylogenetic analyses of the <jats:italic>Yersinia pestis<\/jats:italic> collected from the 12 natural plague foci in China with more than 20 kinds of hosts and vectors. Different ecological landscapes with specific hosts, vectors, and habitat which shape various niches for <jats:italic>Y.\u2009pestis<\/jats:italic>. The phylogeographic diversity of <jats:italic>Y.\u2009pestis<\/jats:italic> in different kinds plague foci in China showed host niches adaptation. Most natural plague foci strains are region\u2010and focus\u2010specific, with one predominant subpopulation; but the isolates from the Qinghai\u2013Tibet plateau harbor a higher genetic diversity than other foci. The <jats:italic>Y.\u2009pestis<\/jats:italic> from <jats:italic>Marmota himalayana<\/jats:italic> plague foci are defined as the ancestors of different populations at the root of the evolutionary tree, suggesting several different evolutionary paths to other foci. It has the largest pan\u2010genome and widest SNP distances with most accessory genes enriched in mobilome functions (prophages, transposons). Geological barriers play an important role in the maintenance of local <jats:italic>Y.\u2009pestis<\/jats:italic> species and block the introduction of non\u2010native strains. This study provides new insights into the control of plague outbreaks and epidemics, deepened the understanding of the evolutionary history of MHPF (<jats:italic>M.\u2009himalayana<\/jats:italic> plague focus) in China. The population structure and identify clades among different natural foci of China renewed the space cognition of the plague.<\/jats:p>","DOI":"10.1002\/ece3.10387","type":"journal-article","created":{"date-parts":[[2023,7,28]],"date-time":"2023-07-28T10:20:20Z","timestamp":1690539620000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["The complex genomic diversity of <i>Yersinia pestis<\/i> on the long\u2010term plague foci in <scp>Qinghai\u2013Tibet<\/scp> plateau"],"prefix":"10.1002","volume":"13","author":[{"given":"Junrong","family":"Liang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention Chinese Center for Disease Control and Prevention  Beijing 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