Among the marine planktonic diatoms, Chaetoceros is among the most species-rich genera, and many Chaetoceros species are considered important primary producers. However, little is known about the ecology and distribution of the few small solitary species within this genus, including Chaetoceros tenuissimus. This article describes a minute Chaetoceros strain, identified as C. tenuissimus (named CT16ED) that was isolated at a coastal lagoon in Corsica Island, Western Mediterranean. The strain was characterized by light microscopy and scanning and transmission electron microscopy, with a specific focus on the fine structure and construction of setae and its behaviour in culture. The CT16ED strain was compared with other strains we isolated from the species type locality (Ostend Harbour, North Sea) by sequencing a fragment of the nuclear ribosomal DNA (rDNA) spanning from the 18S rDNA to the D3 region of the 28S rDNA, and the plastid rbcL gene that codes the large RuBisCO subunit. Based on the literature and the available sequence data, the analysed strains were similar to C. tenuissimus but the phylogenetic analysis indicated a C. tenuissimus species complex that contained several clades, therefore the current taxonomic status of C. tenuissimus is discussed. The comparison with the available rDNA and rbcL sequencing data of strains assigned to species considered as synonyms of C. tenuissimus, including Chaetoceros simplex var. calcitrans, Chaetoceros calcitrans and Chaetoceros calcitrans f. pumilus, suggested that these taxa are paraphyletic within the genus Chaetoceros.