Plague is an infection caused by a Gram-negative bacterium: Yersinia pestis. This organism was isolated in 1894 by the Japanese researcher Shibasaburo Kitasato (a co-worker of Koch) and the Swiss bacteriologist Alexander Yersin (a student of Pasteur) during an epidemic in Hong Kong. The organism has a characteristic shape when stained with Giemsa or Wayson stain: a bipolar rod with a safety pin appearance. The organism is non-motile and forms no spores. The organism grows well on various tissue media. In 1897, the Japanese Masaki Ogata reported that plague was transmitted by rat fleas. In 1898, Paul-Louis Simond during his work in Bombay suspected that the rat flea Xenopsylla cheopis might be the vector. This was confirmed experimentally in 1914 by Bacot and Martin.

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Do not confuse Yersina pestis with Yersinia enterocolitica or Yersinia pseudotuberculosis. These bacteria can provoke enteritis and mesenterial adenitis (swollen lymph nodes in the mesentery, especially near the terminal ileum and the ileocolic junction). Y. pseudotuberculosis is maybe the cause of Izumi fever (pseudoscarlatina).