||Dinoflagellates genomes are large (up to 200 pg) and are encoded in histoneless chromosomes that are quasi-permanently condensed. This unique combination of chromosomal characteristics presents additional topological and cell cycle control problems for a eukaryotic cell, potentially requiring novel topoisomerase activities. The heterotrophic dinoflagellate Crypthecodinium cohnii was used in this study. The topoisomerase II activities throughout its cell cycle were investigated by DNA flow cytometry following enzyme deactivation. Two cIasses of topoisomerase II inhibitors with different inhibitory mechanisms were applied in our study, both of which caused G1 delay as well as G2/M arrest in the C. cohnii cell cycle. The topoisomerase inhibitors amsacrine and ellipticine induced DNA fragmentation in C. cohnii cells. Topoisomerase II activities, as measured by the ability to decatenate kinetoplastid DNA (kDNA), are normally detected throughout the cell cycle in C. cohnii. Fluorescence microscopy and transmission electron microscopy were applied for studying the chromosome morphology and of treated cells. The ultrastructure of dinoflagellate chromosomes were altered upon topoisomerase II deactivation. Our results suggest that the requirement of type II topoisomerase activities during the G1 phase of the cell cycle may relate to the organization of quasi-permanently condensed chromosomes in dinoflagellates. This was also the first time to detect topoisomerase II activity in dinoflagellate cells.