Abstract: Thalassiosira Cleve is one of the most speciose marine diatom genera, that has been globally distributed. To assess the diversity of the genus Thalassiosira species, monoclonal strains were isolated and established from Chinese coast. The morphology was observed by using a light microscope (LM) and a scanning electron microscope (SEM). Sequences of the large subunit (LSU) and small subunit (SSU) of the nuclear rRNA-encoding genes (rDNA) were obtained to form a phylogenetic relationship. Among 14 established Thalassiosira allenii (T. allenii) Takano strains, morphological variation was found involving some with and without marginal ribs on the valve edge. After comparing with the original description of T. allenii, the strains without marginal ribs were assigned as a type of T. allenii, and those with marginal ribs were proposed as a new variety, T. allenii var. striata. Morphological divergence was supported by molecular data as well. On the phylogenetic trees inferred from both LSU and SSU of the nuclear rDNA, accordingly, T. allenii was clustered with var. striata, and formed as sister groups (Bayesian posterior probability (BPP) > 0.90), demonstrating their firm relationship. SSU sequences are totally identical, without any different base pair, between these two varieties. However, 11 different base pairs among 556 LSU base pair, which used for analysis, could be found, and divergence of distance among them is only 0.01.