From the German Bight along Jutland to the western Skagerrak, we found representatives of almost all groups of phycotoxins known to occur in North Sea plankton. Identification was by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) in plankton size fractions, with domoic acid and 20-me G the most abundant toxins. The dominance of 20-me G in the spirolide (SPX) composition of plankton from the Jutland current system matched very well with that of an isolate of the dinoflagellate Alexandrium ostenfeldii. The SPXs of the A. ostenfeldii strain S6_P12_E11, previously isolated from the western North Sea along the Scottish coast, comprised 100% 20-me G, suggesting toxin homogeneity among North Sea populations of this species. We detected highest amounts of azaspiracid-1 in the 3–20-mm size fraction at offshore stations, where the Jutland coastal current converges with the westward North Sea flow off Skagerrak. Azadinium spinosum was subsequently identified by clonal isolation from crude cultures established from these stations. Except for lipophilic toxins usually produced by the dinoflagellate Dinophysis spp., dinophysistoxin-1 (DTX-1) and DTX-2, we detected no other phycotoxins in plankton from the southern German Bight. The spatial distribution of the phycotoxins in the eastern North Sea was apparently related to the hydrographical conditions, identified from salinity and coloured dissolved organic matter profiles. The biogeographical distribution of phycotoxins indicates a strong association with the northward advection by the Jutland current and the mixing of German Bight and North water masses along the northwest Danish coast towards the Skagerrak.