Streptococci bacteria are a fundamental part of the human oral microbiome. Using a competitive mapping approach with ancient DNA from British populations dating 2100BCE-present, we found major shifts in streptococci communities occurred after the post-medieval period. While Streptococcus sp. DD04 now has reduced diversity, Streptococcus sanguinis remains abundant in healthy modern populations where it has acquired genes involved in membrane transport and stress response. These evolutionary histories provide important insights into humanity’s changing oral health.