Unlike other stramenopiles, the anterior flagellum does not bear tripartite tubular hairs. Because this feature is absent, protistologists placed Caecitellus in groups other than the stramenopiles until the kinetid architecture was reconstructed. It may be that other protists that lack flagellar hairs, and whose relationships are presently unknown, are stramenopiles.

The cells are uninucleate. The two flagellar bases of nondividing cells are found just anterior to the nucleus. Several sausage-shaped mitochondria are present; as in other stramenopiles, the cristae are tubular. The cytopharynx is permanently differentiated and prominent. No extrusomes are present on the cell periphery.

There is a single Golgi body anterior to the nucleus and near the flagellar bases.

The cytoskeleton is based on an asymmetrical system of two flagellar bases and three microtubular roots. The arrangement is much like that in the bicosoecids, including Cafeteria.

One of the three microtubular roots arises from the anterior basal body. In most other stramenopiles including Cafeteria, this root has secondary cytoskeletal microtubules associated with it, but in Caecitellus these microtubules have not been found.

The other two microtubular roots arise from the posterior basal body. The compound root R3 arises on the right side of the basal body, initially with ca. 11 microtubules, and then splits into an outer ("x", single microtubule), middle (initially 8 microtubules, adding around 16 more near the cytostome), and inner (three microtubules) subunits. The outer and middle subunits define the outer margin of the cytostome, while the inner subunit defines the margin of the posterior flagellar groove. The R3 root is connected to the two basal bodies by a striated fiber. The R4 root arises on the left side of the posterior basal body. It has two microtubules and terminates in the vicinity of the far end of root R3. The posterior root array is the same as in Cafeteria and other bicosoecids.

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