Abstract: To clarify the species diversity of the genus Thalassiosira, monoclonal strains were isolated and established from the Chinese coast. Morphology was observed using light and electron microscopy and sequences of small and large subunit nuclear ribosomal encoding genes were obtained to build phylogenetic relationships. Among 10 established T. minuscula Takano strains, morphological variations and corresponding molecular divergences were found. After comparison with the original description of T. minuscula, specimens with a rimoportula neighboring one fultoportula were assigned as T. minuscula var. minuscula, and those with a rimoportula neighboring two fultoportulae were proposed as a new variety, T. minuscula var. bicustodis X. H. Guo, Y. Q. Guo & Y. Li. On the phylogenetic trees inferred from small and large subunit nuclear ribosomal encoding genes, T. minuscula var. minuscula was clustered with T. minuscula var. bicustodis as a sister group (BPP > 0.90), thus showing their close relationship. These results, combined with the morphological and molecular data, support the erection of T. minuscula var. bicustodis.