<jats:title>SUMMARY</jats:title><jats:p>To determine its accurate taxonomic position, a tidal pool bloom‐forming dinoflagellate, <jats:italic>Scrippsiella hexapraecingula</jats:italic> was re‐investigated using light, scanning and transmission electron microscopy together with a phylogenetic analysis based on concatenated ribosomal DNA sequences. The culture strains used in this study were established from intertidal rock pool samples taken from Jogashima, Kanagawa prefecture and Heisaura, Chiba prefecture, Japan and were identified as <jats:italic>S. hexapraecingula</jats:italic> originally described by Horiguchi and Chihara from a tidal pool in Hachijo Island, Tokyo, Japan in 1983. The thecal plate arrangement was determined as Po, X, 4′, 3a, 6″, 6c, 5s, 5″′, 2″″. The internal structure was investigated for the first time. The organism has typical dinoflagellate cellular organelles such as a dinokaryotic nucleus, mitochondria with tubular cristae, trichocysts and pusule. The chloroplast was single and connected to the central pyrenoid (stalked type). The eyespot found in the sulcus is of the B type with two rows of superficial intraplastidal lipid globules directly overlain by an extraplastidal single layer of crystalline bricks enveloped by a common membrane. The apical pore is plugged by a double‐layered stub‐like structure. Stalk building material for attachment covered the apical pore. Phylogenetic analysis indicated that <jats:italic>S. hexapraecingula</jats:italic> was most closely related to a freshwater dinoflagellate, <jats:italic>Peridiniopsis borgei</jats:italic>, the type species of the genus <jats:italic>Peridiniopsis</jats:italic>. However, clear differences exist between these two organisms, including their thecal plate arrangement, habitat and habit. As a result, a new genus, <jats:italic>Chiharadinium</jats:italic> Dawut & T. Horiguchi gen. nov. has been proposed rather than attempting to accommodate <jats:italic>S. hexapraecingula</jats:italic> in the genus <jats:italic>Peridiniopsis</jats:italic>. The new combination, <jats:italic>Chiharadinium hexapraecingulum</jats:italic> (T. Horiguchi & Chihara) Dawut & T. Horiguchi comb. nov. has been proposed.</jats:p>