To understand the diversity of the diatom genus Chaetoceros Ehrenberg, the C. lorenzianus complex was previously chosen as a model and three new species were described. In the present study, yet another new species, Chaetoceros pauciramosus sp. nov., was discovered from Chinese tropical waters and the temperate south-eastern Baltic Sea. In the latter locality it has been known since 2003 and identified as C. cf lorenzianus, and now found to comprise a dominating component of the autumn phytoplankton community. Vegetative cells and resting spores were examined by light and electron microscopy. The LSU and SSU of the nuclear rDNA were sequenced. The characters suggesting that C. pauciramosus belongs to C. lorenzianus complex are: 1) the vegetative cells contain four or more chloroplasts, 2) the cells have stiff setae and form regular straight chains, 3) the terminal setae differ in the direction from the intercalary setae. The relationship was well-supported by molecular phylogenetic analyses inferred from both LSU and SSU markers. The primary valve of the resting spore has two conical elevations, each with dichotomously branching processes, similar to other species in the C. lorenzianus complex. Each process forms a tree-like structure with the pointed distal tips which possess one or two thin spikes, that distinguishes C. pauciramosus from allied taxa. In the phylogenetic trees, Chaetoceros pauciramosus clustered with C. elegans, in agreement with their morphologically similar resting spores.