Numerous studies have been conducted on the cellular morphology of Cryptocaryon irritans. However, details regarding the tomont stage of its life cycle remain lacking. In this study, we investigated the morphology of the tomont stage throughout encystment and cell division using light and electron microscopy. Results showed that there was no secretion of encystation-specific secretory vesicles or extrusomes during formation of the cyst wall. Instead, the synthesis and construction of the C. irritans cyst wall materials may involve molecular events at the pellicle. The somatic cilia and the cytostome were present during encystment and covered by the newly formed cyst wall. New somatic cilia were continuously created between old cilia and showed various lengths during cell division, a process that was similar to morphogenesis in many free-living ciliates. During cell division inside the tomont, dividing daughter cells formed temporary cell chains with no oral primordia before separating from each other into dissociative tomite precursors. The process of cell division may not be accompanied by stomatogenesis, and new oral primordia in offspring cells likely formed before the dividing cell chains split into dissociative spherical tomites. Mitochondrial autophagy was observed in encysting C. irritans cells. Numerous endosymbionts and Golgi structures were observed in the tomont cytoplasm. Cellular metabolic activity in the C. irritans tomont was quite high, with large amounts of materials or cellular organelles potentially being synthesized and prepared for the following infective theront stage.