Clipperton Island is a small French coral atoll in the eastern Pacific Ocean, which has been rarely investigated because of its remote location and difficult access. There is little scientific information on this ecosystem and only a few microalgae have been reported from the lagoon. To date, only one dinoflagellate taxon, Peridiniopsis cristata, is known to inhabit the lagoon. During an expedition in 2005 to study the lagoon and the surrounding oceanic waters of Clipperton Island, a further investigation of the lagoon phytoplankton was undertaken. In addition to P. cristata, which was still abundant in the upper water layer, two other thecate dinoflagellates were recorded. One dinoflagellate was identified as Durinskia baltica, while the other had the same thecal plate arrangement as P. cristata but was slightly smaller, (27) 30–40 μm long, 26–32 μm wide, and its plates were unornamented and devoid of prominent lists. Hence, the latter taxon is described as P. cristata var. tubulifera since it represents an extreme variation in the ornamentation of the nominate variety. This study provides a description and detailed illustrations of the three taxa found in this peculiar tropical marine ecosystem.