A new species of Scrippsiella is described by light and electron microscopy from laboratory cultures established from resting cysts collected from the southeast coast of Iran. Comparative morphological analyses and sequencing of the rDNA-ITS and 5.8S rDNA show that the new species, Scrippsiella irregularis sp. nov., is allied to but distinct from Scrippsiella precaria and S. ramonii. Vegetative cells of the new species are similar in size, shape, and plate tabulation to S. precaria; however, the cingulum is equatorially placed, the nucleus is in the hypocone, and the second anterior intercalary plate is larger and rounded rather than diamond-shaped. The resting cysts isolated from sediments and produced in laboratory cultures are spherical to ovoid with numerous pointed to slightly capitate calcareous processes.