The nucleotide sequence for the Saccharomyces cerevisiae gene TOP2, which encodes DNA topoisomerase II, was compared with the sequence for bacterial DNA gyrase. The amino and carboxyl terminal halves of the single-subunit yeast enzyme showed homologies with the B and A subunits of bacterial gyrase, respectively, at corresponding positions along the polypeptide chains. Although the two enzymes differ in both quaternary structure and activity, the homology between the two proteins indicates mechanistic as well as structural similarities, and a probable evolutionary relationship.