In order to explore the diversity of the genus Thalassiosira, live samples were collected from Chinese coastal waters and monoclonal strains were established. Based on the combination of morphology and molecular data of ribosomal DNA genes, a novel species, Thalassiosira secreta sp. nov. Yang Li & Y.Q. Guo, was described from the South China Sea. The most conspicuous feature of T. secreta is 5–7 fultoportulae located inside on the inner walls of the central areola. Two rings of siliceous spines are seen; one on the edge of the valve face, and another on the mantle. A rimoportula with a remarkable external tube, is positioned on the edge of the valve face, as part of the ring of spines on the valve edge. A ring of fultoportulae is located on the valve mantle, distal from the ring of spines on the mantle, with one fultoportula corresponding to each spine. The areolae on the valve face are arranged in a linear pattern. Morphologically, T. secreta resembles T. nodulolineata, T. densannula, T. nanolineata, T. incerta and T. wongii, all having several fultoportulae surrounding the central areola. This is partly supported by the phylogenetic analyses, as T. secreta clustered together with T. nodulolineata, whereas the sequences of the remaining taxa are unavailable presently. The positions of the central fultoportulae differ among the above allied taxa, as they are ‘hidden’ on the inner wall of the central areola in T. secreta, but located on the external wall of the central areola in the remaining taxa. All these morphologically related taxa may represent a new subgroup within the genus Thalassiosira, but this needs to be confirmed by molecular data. The taxa are all characterized by several fultoportulae surrounding the central areola.