FtsK and topoisomerase (Topo) IV are both involved in chromosome segregation in Escherichia coli. The former protein resides at the septal ring and is required for resolution of chromosome dimers. The latter protein is the chromosomal decatenase. We have demonstrated recently that Topo IV activity is concentrated at the septal proximal regions of the nucleoids late in the cell cycle. Here we demonstrate that FtsK and Topo IV physically and functionally interact. Topo IV was recovered in immunoprecipitates of FtsK. Two-hybrid analysis and immunoblotting showed that this interaction was mediated by the ParC subunit of Topo IV. In addition, we show that the C-terminal motor domain of FtsK stimulates the decatenation activity of Topo IV but not that of DNA gyrase, the other type II topoisomerase in the cell. Topo IV and FtsK appear to cooperate in the cell as well. Rescue of a parE temperature-sensitive mutation by overproduction of DnaX, which leads to stabilization of the temperature-sensitive Topo IV, required both the C-terminal domain of FtsK and dif, whereas rescue by overproduction of Topo III, which bypasses Topo IV function, did not. The interaction between FtsK and Topo IV may provide a means for concentrating the latter enzyme at the cell center.