Species within the diatom genus Pseudo-nitzschia (Peragallo) have been identified as producers of domoic acid, the toxin responsible for amnesic shellfish poisoning. Toxin- and non-toxin-producing species of Pseudo-nitzschia have been reported globally; however, as Pseudo-nitzschia species cannot be routinely identified to species level using light microscopy, cells are rarely recorded to species level during long-term monitoring studies. Here, we report the results of a comparative survey of Pseudo-nitzschia species at two monitoring sites in the North Sea: Stonehaven on the east coast of Scotland and Helgoland Roads in the German Bight. A difference in the seasonality of this genus was observed between the sites with Pseudo-nitzschia cells playing a major role in the spring bloom as well at the summer and autumn diatom community at Stonehaven. In contrast, Pseudo-nitzschia was abundant only during the summer months at Helgoland. Pseudo-nitzschia cells constitute a higher proportion of the diatom community at Stonehaven than at Helgoland, particularly during the late summer, autumn and winter and thus may be considered more ‘ecologically important’ at this site. A total of eight different species were recorded during this survey with five Pseudo-nitzschia species observed at the Helgoland site: P. pungens, P. fraudulenta, P. americana, P. cf. delicatissima and the potentially toxic species P. multiseries. Six species were also recorded at Stonehaven; P. australis, P cf. delicatissima, P. pungens, P. cf. pseudodelicatissima, P. subpacifica and P. seriata. This study represents the first examination of the seasonality of Pseudo-nitzschia species around Helgoland and the first comparison between two long-term monitoring sites in the North Sea. P. americana and P. multiseries are also recorded at the Helgoland Roads time-series site for the first time.