We describe the sexual reproduction and breeding behaviour of a novel sigmoid pennate diatom Nitzschia siwaschica sp. nov. To date, sexual reproduction has been described in 21 representatives of the highly heterogeneous genus Nitzschia, including three sigmoid freshwater species. Nitzschia siwaschica originates from a hypersaline environment. The specific growth rate of N. siwaschica weakly depended on salinity levels, varying from 0.75 to 0.99 divisions per day, across salinity levels from 10 to 100 psu. This diatom exhibited heterothallic sexual reproduction. Compatible pairs of clones were able to reproduce sexually in the relatively broad range of salinities, 20–80 psu. According to Geitler’s classification, the pattern of sexual process in this species (cis-anisogamy) corresponds to type IA2b. Furthermore, we determine the phylogenetic relationships of N. siwaschica with other Nitzschia species to provide a comprehensive understanding of the species’ evolutionary position.