Cryptomonas sp. Φ is an undescribed cryptomonad used for many studies into the endosymbiotic origin of plastids. Cryptomonas sp. Φ was characterized using electron microscopy, DNA sequencing and karyotyping. DNA sequence data show that Cryptomonas sp. Φ has been confused with the related cryptomonad, Guillardia theta, which is the organism actually used in most published studies on cryptomonad endosymbiosis to date. It is proposed that the strain Cryptomonas sp. Φ be recognized as a distinct species under the name Hanusia phi. Although Hanusia phi shares molecular and karyotypic features with G. theta, it cannot be assigned to Guillardia because it does not fit the morphological description of this genus. H. phi differs from G. theta in periplast structure, configuration of the furrow-gullet system, and cell size. Morphologically, however, H. phi is very similar to Teleaulax acuta, Teleaulax merimbula and the diplomorph of Proteomonas sulcata.