The Uruguay River is one of the largest rivers in South America (>1,800 km long, annual discharge 6230 m3.s–1). It belongs to the La Plata Basin and its lower part flows between two countries, Argentina and Uruguay. The water quality and flow rate is affected by more more than twenty hydropower dams, increasing urbanization and the expansion of agriculture. These effects, together with climate variations favour the proliferation of massive blooms of planktonic cyanobacteria. These cyanobacterial blooms usually contain several Dolichospermum morphospecies. Dominance of one of them, preliminarily determined as D. cf. pseudocompactum, was previously reported (Ferrari et al. 2011). Morphological characteristics of this morphospecies are similar to D. pseudocompactum (M. Watanabe 1996) Wacklin et al. 2009 in some points, but do not fully correspond with its description, neither with definitions of any Dolichospermum species described so far.