The Raphidophycean Fibrocapsa japonica Toriumi & Takano was detected for the first time offshore in the Eastern Alboran Sea (Western Mediterranean) in October 2006. Its distribution appeared very localised and atypical, as it was abundant only in the open waters of a cyclonic eddy. Microscope counts of the natural phytoplankton assemblages revealed that F. japonica was dominant in the microplankton, together with Dinophyceae, within and below the cyclonic nutrient-rich dome (25 - 30 m). Bacillariophyceae were the primary microplanktonic fraction in only a few samples. Moderately high abundances of F. japonica (maximum of 60 cells ml-1), with preliminary cysts and many cells aggregated in mucous nets, indicated a senescent phase. We also suggest a Mediterranean origin for this species. This was confirmed by molecular identification and by a water temperature of 15 °C, which could have favoured pre-cyst formation. Finally, we hypothesise that F. japonica, which is generally a coastal species, could have a coastal origin. Since F. japonica was confined to the cyclonic waters, which typically derive from coastal waters, it was collected at a depth of 40-60 m at the coastal sites and it is generally a coastal species, we hypothesise that it could have a coastal origin and it was entrapped by the cyclonic eddy, which could have carried offshore this harmful species.