The fine structure of vegetative cells and resting spores of Rhizosolenia minima Levander from three Tyrrhenian brackish-water lagoons has been investigated by electron microscopy. The species has none of the morphological characters typical of the genus Rhizosolenia Ehrenberg and appears to be closely related to Miraltia throndsenii Marino, Montresor & Zingone which belongs to the family Chaetoceraceae (sensu Simonsen 1979) or Chaetocerataceae (sensu Round et al. 1990). In a few natural samples from the Gulf of Naples, a new variety of the latter species possessing three setae has been found, co-occurring with the already described morphotype. Therefore, both varieties are transforred to the genus Chaetoceros Ehrenberg (sub-genus Hyalochaete) as C. throndsenii var. throndsenia (Marino, Montresor & Zingone) Marino, Montresor & Zingone comb. nov. and C. throndsenii var. trisetosa Zingone var. nov. Based on the fine morphology and the occasional presence of a third seta (van Goor 1924) the inclusion of Rhizosolenia minima in the genus Chaetoceros is also proposed.The relationships between C. throndsenii and C. minimus (Levander) comb. nov. and other small, weakly silicified Chaetoceros species (sub-genus Hyalochaete), which form resting spores, were also studied. In light microscopy, the closest related species appears to be Chaetoceros subtilis Cleve, including the solitary form C. subtilis var. abnormis f. simplex Proschkina-Lavrenko which has a single seta per cell. However, TEM observations revealed clear differences in the ultrastructural features of the valves and setae.The amended diagnosis for the species C. minimus, and the diagnosis for C. throndsenii var. trisetosa are given.