Genus Amphidinium Claparède et Lachmann (Gymnodiniales, Dinophyceae) sensu lato has recently undergone a reappraisal using extended microscopical methods and genetic comparisons, with the type species and morphologically similar species used for the redescription of the genus Amphidinium sensu stricto. Within the latter concept of the genus, the new species Amphidinium thermaeum is established using light and scanning electron microscopy in combination with LSU rDNA phylogeny. This species was isolated from the Thermaikos Gulf in Greece, and its description is largely based on observations of cultured material. The main diacritic features distinguishing A. thermaeum from related taxa were: shape, size and plasticity of the cell, position of distal and proximal cingulum ends, site of longitudinal flagellar insertion, sulcal course, pusule details, plastid characteristics, and mode of cell division. Genetic phylogeny applying Bayesian Inference, Maximum Likelihood, and Neighbor-Joining analyses, places A. thermaeum in an independent position within the Amphidinium sensu stricto monophyletic group, and the new species is closely related to its small and morphologically similar siblings (A. massartii, A. klebsii, A. trulla, A. gibbosum, A. carterae).