The identifying features of Chrysochromulina brevifilum are clarified, based on a detailed ultrastructural investigation. The light microscopical observations in the type description are confirmed, and the first description of all three scale types (spine scales and large and small plate scales) is provided. The general ultrastructure and arrangement of the organelles do not differ from those of most other prymnesialean motile cells, but the transitional region of each flagellum has an unusual 'spoked' arrangement distal to the 2 transitional plates. The flagellar apparatus has 2 main distal connectives (with extensions from the distal band ventrally over the R2 microtubular root, anteriorly towards the R1 broad root, and posteriorly towards the left chloroplast), 3 proximal connectives, and 4 different microtubular roots of which the RI descends posteriorly and ventrally as a cytoplasmic tongue. This flagellar apparatus is compared with others in the genus and order, but the variation between species and genera is too wide to enable any phylogenetic conclusions to be made.