A new culture strain of Navicula veneta Kützing (Bacillariophyceae) was isolated from brown mats covering thermal muds in the SPA town of Abano Terme, Padova, Italy. The morphology, 18S rDNA and rbcL gene sequences of this strain were analysed. The results do not support an existing taxonomic proposal to lower the taxonomic rank of Navicula veneta to a variety of Navicula cryptocephala Kützing. Therefore, we consider Navicula veneta as a good species in its own right. We also hypothesize that the species Navicula veneta, as defined morphologically, contains a number of cryptic species yet to be discovered and analysed genetically.