Abstract: Thalassiosira Cleve is one of the largest genera of diatoms, and its taxa are widely distributed in global waters. The present taxonomic and systematic theories of Thalassiosira have been established on the basis of morphology. Most morphological traits provide important taxonomic significance, especially ultra-morphology under electron microscopy. However, variation in some key morphological features has been reported, and the value in taxonomic application has become somewhat suspect. Here, a widely distributed species, T. allen Takano, was selected to re-examine certain traits inferred from morphological and molecular analysis based on established monoclonal strains. Results showed that: (1) The arrangement pattern of the areolae in T. allen varied normally, exhibiting tangential or eccentric array. Different locations of rimoportulae were found, replacing the place of one marginal fultoportula, or at the middle between two, or close to one marginal fultoportula. These two features varied considerably, and thus their taxonomic significance has become somewhat limited. (2) No rib was observed at the valve margin, which could be applied as a typical trait to distinguish T. allen and close taxa. (3) No pseudo-cryptic or cryptic species were found in T. allen due to their conservative genetic divergence. Combined with previous studies, some morphological traits were reassessed. Areolae arrangement varied frequently and was easily affected by environmental factors, and thus was not a good taxonomic trait for Thalassiosira taxa classification. Processes were key features for Thalassiosira taxa, because most traits were steady, especially the amount, location, and density of the fultoportulae. However, the location of the rimoportulae varied in some Thalassiosira species, and should be cautiously applied. Ribs were a relatively stable trait for T. allen and several other Thalassiosira taxa, and could be applied in taxonomic classification. Molecular data can play a key role in the re-examination and re-evaluation of morphological traits, while inadequate information remains a limitation for further study. In summary, this research provides a useful reference for the re-evaluation of the taxonomic significance of key morphological traits and renews the usage of these traits in present taxonomy.