The body scales of 12 Heterocapsa species including a new species, H. pseudotriquetra Iwataki, Gert Hansen & Fukuyo, sp. nov. were investigated by transmission electron microscopy to clarify ultrastructural differences. All species had scales with a body-scale structure consisting of a triradiate basal plate and a three-dimensional construction composed of vertically standing uprights or spines and horizontal bars. This basic scale structure is considered to be a generic characteristic. Finer scale details such as the shape and presence of a central hole in the basal plate, the numbers of uprights, bars and spines are considered to be species-specific. Two types of scales were found within clonal cultures of H. arctica and H. circularisquama and it is suggested that these represent ‘mature' and ‘immature' body scales. Intraspecific variation of the basal plate ‘reticulation' was also observed. This variation was particularly evident in prolonged cultures of H. horiguchii and H. rotundata. The body-scale structure of 11 described species can be distinguished. However, two species, namely H. triquetra and H. pseudotriquetra, have the same scale morphology and are distinguished by differences in cell shape and LSU rDNA (25S rDNA) sequences.