Yersinia pestis, the causative agent of plague, is thought to have arisen from the less virulent enteric bacterium Yersinia pseudotuberculosis between 2,600 and 28,000 years ago. Until now, Y. pestis had not been recovered from human remains older than 1,500 years. Now, a report identifies Y. pestis in the teeth of 7 (out of 101) Eurasian individuals dating from 2,800 to 5,000 years ago. Notably, the Y. pestis genomes from these Bronze Age individuals all lacked ymt, the gene encoding a phospholipase that is essential for bacterial survival in the flea vector, which is responsible for transmission of bubonic plague. Furthermore, the ancient Y. pestis genomes encoded the Pla protein, which is essential for deep tissue invasion, but they lacked an isoleucine-to-threonine mutation that is essential for developing bubonic plague. These data suggest that a less pathogenic Y. pestis was already endemic in humans before it acquired genetic changes that enabled bacterial survival in the flea vector and deep tissue invasion, which gave rise to more virulent strains responsible for pandemic bubonic plague.