Life evolved in an anaerobic world; therefore, fundamental enzymatic mechanisms and biochemical pathways were refined and integrated into metabolism in the absence of any selective pressure to avoid reactivity with oxygen. After photosystem 2 appeared, environmental oxygen levels rose very slowly. During this time microorganisms acquired oxygen tolerance by jettisoning enzymes that use glycyl radicals and low-potential iron-sulfur clusters, which can be directly poisoned by oxygen. They also developed mechanisms to defend themselves against O 2 − and hydrogen peroxide, partially reduced oxygen species that are generated as inadvertent by-products of aerobic metabolism. These species are more chemically reactive than is molecular oxygen itself. Contemporary organisms have inherited both the vulnerabilities and the defenses of these ancestral microbes. Current research seeks to identify these, and bacteria comprise an exceptionally accessible experimental system that has provided the many of the answers. This manuscript reviews recent developments and identifies remaining puzzles.