Abstract: As one of the largest marine planktonic diatom genera, Chaetoceros Ehrenberg has a very wide biogeographi-cal distribution from polar to tropical waters. C. decipiens Cleve is a representative species of the genus Chaetoceros characterized by the regular chains and stiff setae. The fusing part on the sibling setae bases was the unique characters for C. decipiens in the present taxonomy system that mainly built on morphology, which has been accepted and used by some diatom taxonomists. However, some other researchers hold different opinion, in which the fusing on the sibling setae bases was a variable morphological structure that could not give much significant taxonomic value. Meanwhile, some questions remain about the taxonomic position of the intraspecific units of C. decipiens, which is difficult to answer whether these intraspecific units are independent taxonomic units or just a living stage of life cycle of C. decipiens. To answer this question, the monoclonal stains and the combination of morphology features and molecular analy-sis will be required. To do this, several monoclonal strains were established from several Chinese representative sites using glass micropipette under invert microscopy according with the present taxonomic morphology of C. decipiens. The morphology was studied by light microscopy, scanning electron microscopy and transmission electron microscopy. Meanwhile, the hypervariable region (D1-D3) of nucleic large subunit ribosomal rRNA encoding gene was amplified and sequenced as molecular evidence. The result indicated that the fusing of sibling setae base was not a steady structure, which could not be considered as significant morphological feature for the accurate identification of C. decipiens, and that some similar species without fusing of sibling setae base could be the true C. decipiens. Moreover, according to the molecular phylogenetic analysis, high diversity was hidden in the morphologically-identified C. decipiens and C. lorenzianus, which might show the presence of cryptic and pseudo-cryptic species. Inaddition, C. decipiens f. singula-ris Gran was confirmed as a temporary stage of whole life cycle of C. decipiens based on the continuous observation during cultures maintainance. Finally, they totally shared the same LSU sequences. Thus, C. decipiens f. singularis Gran was proposed as the synonym of C. decipiens.