The life cycle of the unicellular eukaryote Eufolliculina uhligi includes two structurally and physiologically different cell types: a motile swarmer that is arrested in the cell cycle, and a sessile cell (trophont) that feeds and reproduces. These two cell types offer an exceptionally favourable system for the isolation of genes involved in cell cycle regulation and cellular morphogenesis. Differential screening of a trophont cDNA library using a swarmer-subtracted, trophont-specific probe yielded eleven clones that represent trophont-specific transcripts and one clone that represents a swarmer-specific transcript. Sequence analysis showed that seven clones, including the only swarmer-specific one, represent unknown genes, whereas five clones could be identified by sequence comparisons. Two of the clones appear to encode proteins that are involved in the regulation of growth and metabolism. The deduced sequences of three clones resemble potential cell cycle regulators. Data are presented on a putative member of the calcium/calmodulin-dependent protein kinase family and on a TIP120-like sequence, which is the first such sequence to be described since the discovery of the rat TIP120 protein. Furthermore, a unique new sequence is presented, whose features suggest that it represents a protein that is involved in the regulation of cell division. It includes domains characteristic of two different protein families, cyclin-dependent kinases (CDKs) and cyclins, both of which are known to be cell cycle regulators. Based on our results we propose a model for cell cycle regulation in ciliated protozoa.