The genus Cryptomonas is easily recognized by having two flagella, green brownish color, and a swaying behavior. They have relatively simple morphology, and limited diagnostic characters, which present a major difficulty in differentiating between species of the genus. To understand species delineation and phylogenetic relationships among Cryptomonas species, the nuclear-encoded internal transcribed spacer 2 (ITS2), partial large subunit (LSU) and small subunit ribosomal DNA (rDNA), and chloroplast-encoded psbA and LSU rDNA sequences were determined and used for phylogenetic analyses, using Bayesian and maximum likelihood methods. In addition, nuclear-encoded ITS2 sequences were predicted to secondary structures, and were used to determine nine species and four unidentified species from 47 strains. Sequences of helix І, ІІ, and ІІІb in ITS2 secondary structure were very useful for the identification of Cryptomonas species. However, the helix ІV was the most variable region across species in alignment. The phylogenetic tree showed that fourteen species were monophyletic. However, some strains of C. obovata had chloroplasts with pyrenoid while others were without pyrenoid, which used as a key character in few species. Therefore, classification systems depending solely on morphological characters are inadequate, and require the use of molecular data.

Rhinomonas reticulata var. atrorosea G. Novarino is a photosynthetic marine flagellate that is known to have typical characteristics of cryptomonads. We examined the flagellar apparatus of R. reticulata var. atrorosea by transmission electron microscopy. The major components of the flagellar apparatus of R. reticulata var. atrorosea consisted of four types of microtubular roots (1r, 2r, 3r, and mr), a non-keeled rhizostyle (Rhs), mitochondrion-associated lamella (ML), two connections between basal bodies, a striated fibrous root (SR) and a striated fiber-associated microtubular root (SRm). Four types of microtubular roots originated near the ventral basal body and extended toward the left side of the basal bodies. The non-keeled Rhs originated at the Rhs-associated striated fiber, which was located between two basal bodies and extended into the middle of the cell. The ML was a plate-like fibrous structure associated with mitochondria and originating from a Rhs-associated fiber. It split into two parts and extended toward the dorsal-posterior of the cell to a mitochondrion. The SR and SRm extended parallel to the anterior lobe of the cell. The overall configuration of the flagellar apparatus in R. reticulata var. atrorosea was similar to the previously reported descriptions of those of Cryptomonas paramecium, C. pyrenoidifera, C. ovata, Hanusia phi, Guillardia theta, and Proteomonas sulcata. However, the flagellar apparatus system of R. reticulata var. atrorosea was more complex than those of other cryptomonad species due to the presence of an additional microtubular root and other distinctive features, such as a rhizostyle-associated striated fiber and large ML.