A new heterotrophic sand-dwelling dinoflagellate, Ankistrodinium armigerum K. Watanabe, Miyoshi, Kubo, Murray et Horiguchi sp. nov., is described from Ishikari Beach, Hokkaido, Japan and Port Botany, NSW, Australia. The dinoflagellate is laterally compressed, possessing a short triangular epicone and a large sac-like hypocone. It possesses a right-handed cingulum and a deeply-incised sulcus. The sulcus descends towards the posterior of the cell where it becomes much deeper and wider, resulting in a bilobed ventral side to the hypocone, with a greater excavation of the left lobe than the right. In addition, the right lobe of the hypocone is shorter than the left lobe, which allows a partial view of the left sulcal wall when the cell is viewed from its right side. The sulcus ascends in the epicone to form an apical groove. The apical groove is linear but terminates in an ellipsoid fashion and its extremity approaches, but does not form a closed loop with the apical end of the linear portion. The dinoflagellate possesses two distinct size classes of trichocysts. The large trichocysts are located in the posterior part of the cell, while small trichocysts are distributed throughout the cell. The dinoflagellate shares morphological characteristics with the heterotrophic sand-dwelling dinoflagellate, Ankistrodinium semilunatum, the type species of the genus. These include a laterally compressed cell, a right-handed cingulum, a deeply-incised sulcus and the same basic structure to the apical groove. Molecular phylogenetic analyses based on small and large subunits of rDNA showed that in both trees, A. semilunatum and A. armigerum formed a robust clade, suggesting that these two species are closely related. Because no organism with the characteristics of this species exists and because this species is closely related to A. semilunatum, we concluded that this species should be described as a second species of the genus Ankistrodinium.