The genus Scrippsiella contains approximately 20 species that are widespread in coastal and oceanic areas. Classification of Scrippsiella traditionally relied on cyst morphology because the plate pattern was rather conserved. A new species, S. enormis sp. nov. was obtained by incubating a noncalcified cyst from sediments collected in the East China Sea. The vegetative cells consisted of a conical-convex epitheca and a round hypotheca with the plate formula of po, x, 4′, 3a, 7″, 6c (5c+t), 5s, 5′″, 2″″. It differed from other Scrippsiella species by possessing an asymmetrical 1' and generating noncalcareous, spherical cysts with paratabulation. Phylogenetic analyses based on internal transcribed spacer (ITS) and 5.8S rDNA sequences revealed that S. enormis was nested within the Calciodinellum clade. In addition, two strains of S. cf. spinifera (strains SSFC02, SSFC03) were obtained by incubating calcareous cysts from sediments collected in the South China Sea. They shared identical ITS sequence and formed a sister clade of the S. trochoidea species complex, suggesting little phylogenetic significance of antapical spines in Scrippsiella.