Dinoflagellates in the genus Symbiodinium are known as zooxanthellae and exist as either symbiotic or free-living forms. Among this genus, two species, Symbiodinium minutum and Symbiodinium psygmophilum, were recently established based on genetic characters. However, some critical morphological characters of these species, such as plate formulae and related diagnoses have not been provided yet. In this study, we analyzed the morphology of S. minutum and S. psygmophilum by scanning and transmission electron microscopy. The S. minutum had the Kofoidian plate formula consisting of a small plate (x), elongated amphiesmal vesicle (EAV), 4ʹ, 5a, 8ʹʹ, 7s, two cingulum rows, 18-20c, 6ʹʹʹ, and 2ʹʹʹʹ, while S. psygmophilum had x, EAV, 4ʹ, 5a, 8ʹʹ, 7-10s, two cingulum rows, 20-22c, 5-6ʹʹʹ, and 1ʹʹʹʹ. These plate formulae are different from any other reported Symbiodinium species. In addition, both species had a pentagonal 1a plate and a hexagonal 2a plate, while other known Symbiodinium species had a hexagonal 1a plate and a pentagonal 2a plate. Thus, we confirm the species status of S. minutum and S. psygmophilum based on morphological and genetic characters and report the detailed morphological characteristics of these two species.