An unknown parasitic protist is described in the free-living cryptophyte Chilomonas paramaecium. The biflagellated sporozoite has an elongated shape with an apical complex and a central nucleus. The pair of flagella are inserted at the base of the pseudo-conoid, and two microtubular roots situated underneath the plasma membrane are attached to each basal body. The apical complex comprises a set of 10-14 micronemes and a train of dumb-bell vesicles which converge toward the tip of the pseudo-conoid. Micronemes are outlined by a four-microtubule fibre and the train of vesicles is associated with a three microtubule in a rake-like fibre. The mitochondrial network has few cristae and a fairly reduced dense matrix. A large vacuole containing microfilamentous material is connected to the nuclear envelope and the Golgi body is situated close to the nucleus. The life cycle begins with the adhesion of the anterior tip, followed by the penetration of the flagellated sporozoite in a specialized region at the base of Chilomonas flagella. The trophont grows within the host cytoplasm, and after 4-5 successive nuclear mitoses, the trophozoites/sporozoites bud on the surface, while they acquire flagella, micronemes and other apical structures. The mitosis is closed with an external spindle lacking a paradesmosis. There is no sporangium, but a resting-cyst was sometimes observed inside the host. This parasite is phylogenetically affiliated to the Perkinsozoa lineage comprising Perkinsus and Parvilucifera. The new genus Cryptophagus is created for this parasite.