The diatom Chaetoceros cf. lorenzianus was found for the first time in the southern Baltic Sea: in November 2003 in the Gulf of Gdańsk and in October 2005 in the Lithuanian coastal waters. The nearest known location of the species is in the Kattegat and the Belt Sea area, approximately 500 km to the west and the discontinuity implies a non-indigenous distribution of this species. Since its appearance in the Polish and Lithuanian waters, C. cf. lorenzianus has been documented each year from September until November–December, usually reaching a maximum abundance between the end of September and the beginning of November. The highest abundance observed was 1.2 × 106 cells l−1, corresponding to a biomass of 3.3 × 103 μg l−1, which accounted for more than 70% of the diatom biomass and caused C. cf. lorenzianus to dominate the diatom community. In October of 2006, 2008 and September 2009–2011, large abundances of the characteristic resting spores of typical C. lorenzianus were observed. However, many of the cells possessed features of both C. lorenzianus and Chaetoceros decipiens, suggesting that the population may be an intermediate form. This study is important as C. cf. lorenzianus is new to the southern and south-eastern Baltic Proper and has become an important member of the autumn phytoplankton community.