Qualitative differences between interphase and mitotic topoisomerase II were studied in Chinese hamster ovary cells. Differences in sites of phosphorylation of in vivo 32P-labeled topoisomerase II alpha were observed between mitosis and interphase by one-dimensional phosphopeptide mapping of partial tryptic digests. Two-dimensional phosphopeptide mapping of complete trypsin digests revealed two phosphopeptides unique to interphase and three phosphopeptides unique to mitosis. A reduced electrophoretic mobility on denaturing gels (approximately 190 kDa) was observed for the beta-isoform of topoisomerase II in mitosis relative to interphase. Treatment of lysates with alkaline phosphatase demonstrated that this was due to phosphorylation of mitotic topoisomerase II beta. The existence of interphase- and mitosis-specific sites of phosphorylation of topoisomerase II alpha, along with the electrophoretic mobility shift caused by phosphorylation of topoisomerase II beta in mitosis, demonstrates qualitative differences between interphase and mitosis in the phosphorylation state of both isoforms of topoisomerase II.