[3] Cryptophytes are distinguished by the presence of characteristic extrusomes called ejectosomes or ejectisomes, which consist of two connected spiral ribbons held under tension.

Large ejectosomes, visible under the light microscope, are associated with the pocket; smaller ones occur underneath the periplast, the cryptophyte-specific cell surrounding.

Some Cryptomonas species may also form immotile microbial cysts–resting stages with rigid cell walls to survive unfavorable conditions.

Cryptophyte flagella are inserted parallel to one another, and are covered by bipartite hairs called mastigonemes, formed within the endoplasmic reticulum and transported to the cell surface.

The group have evolved a whole range of light-absorbing pigments, called phycobilins, which are able to absorb wavelengths that are not accessible to other plants or algae, allowing them to live in a variety of different ecological niches.

[9] An ability that originates from the evolution of a unique light‐harvesting antenna complex derived from two relict parts of the red algal phycobilisome, which was completely dismantled during the endosymbiotic process.