Recent studies have described several new species within the section Compressa of the genus Chaetoceros. To explore the diversity in the section, further studies were conducted based on monoclonal strains established from Chinese warm waters. A combination of molecular and morphological data showed the presence of a new species, Chaetoceros brevispinosus, within the section. Morphologically, C. brevispinosus is characterised mainly by the morphology of the resting spore. The primary valve is convex with numerous short spines, whereas the secondary valve has a more centrally placed vault with less developed spines and ridges. Chaetoceros brevispinosus constitutes a distinct lineage on the LSU and SSU phylogenetic trees, and forms a sister taxon to C. contortus cf. var. contortus. In the phylogenetic analyses, C. contortus var. ornatus formed a distinct lineage and did not form a sister clade to C. contortus cf. var. contortus. Nine and six different base pairs, as well as a genetic distance of 0.012 and 0.008, separated C. contortus var. ornatus and two clades of C. contortus cf. var. contortus. Morphological differences, based on vegetative cells and resting spores, are still uncertain as the morphology of C. contortus var. contortus needs to be examined based on material from the type locality. Chaetoceros contortus var. ornatus makes up the sister taxon to C. bifurcates on the LSU tree. Hence, we propose that C. contortus var. ornatus be raised to species level as C. ornatus stat. nov.