A small-sized, peridinin-containing, athecate dinoflagellate (13–17 µm long) was isolated into clonal culture from a water sample collected at a nearshore location in Tenerife, Spain (October 2004). Based on phenotypic characters (size, shape, pyrenoid and nucleus position), the culture was identified as Gyrodinium oblongum. However, a detailed ultrastructural examination revealed a number of features that did not fit into the current delineation of the genus Gyrodinium or any other dinoflagellate. Likewise, the molecular phylogeny and sequence divergence estimates based on partial LSU rDNA sequences indicated that this isolate has a taxonomically isolated position, and we therefore propose the new genus Moestrupia to accommodate this species within the Dinophyceae. The ultrastructural study uncovered a number of unique features for Moestrupia, for example, a microtubule supported ventral flange situated along the right cingular border and onto the episome. Also, the exit point of the peduncle, through a lip-like protrusion situated in a cavity on the episome, is new in dinoflagellates. The transverse flagellum appeared less coiled compared to other dinoflagellates, and its distal end terminated some distance within the wide sulcus. The upper cingulum border had a distinct rim supported by microtubules; whereas, the lower cingulum border was indistinct. The apical groove was short and curved and bordered on each side by a delicate rim, which may represent amphiesmal vesicles. It ran from the anterior part of the ventral flange to the middorsal side of the episome. Thus, it differs markedly from that in species of Gyrodinium and emphasizes it being distantly related to this genus