Rhodomonas salina is a phototrophic marine flagellate. We examined the ultrastructure of R. salina with particular attention to the flagellar apparatus by transmission electron microscopy and compared it with that of other cryptomonads reported previously. The major components of the flagellar apparatus in R. salina were a keeled rhizostyle (Rhs), a striated fibrous root (SR), a SR-associated microtubular root (SRm), a mitochondrion-associated lamella (ML), and three types of microtubular roots (9r, 4r, and 2r). The keeled Rhs originated near the proximal end of the dorsal basal body, passed near the nucleus and dissociated at the posterior end of the cell. The SR and SRm originated between two basal bodies and laterally extended to the right side of the cell. The ML originated between two basal bodies and extended to the left side of the cell. The 9r originated between the ventral basal body and the Rhs and extended toward the anterior dorsal lobe of the cell. The 4r originated near the 9r and extended toward the dorsal lobe with the 2r, which originated between two basal bodies. Here, the flagellar apparatus in R. salina is described, and the ultrastructure of the flagellar apparatus is compared among cryptomonad species.