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Background and aims: In 2013, blooms similar to those produced by Didymosphenia geminata (Lyngbye) M. Schmidt around the world, were detected in the Grande River basin, Tierra del Fuego province, and in 2014 in de las Vueltas River in Santa Cruz province. The aim of this paper is to analyze the valve morphology and morphometry of these materials to establish if they correspond to D. geminata or to other species of the genus that is producing the massive growth in southern Patagonia. M&M: Samples were collected at Grande River in 2013 and 2015 and, in de las Vueltas River in 2015 and 2016. Samples were analyzed with light and electron microscopy. For morphometric analyses 100 specimens from each sample were measured and statistical analyses were carried out using the R statistical package. Results: The studied populations have the same fine morphology described for other populations collected in Patagonia. Nevertheless, in some sampling sites from Santa Cruz province, we found a morphotype with a markedly smaller size, subcapitated poles, little marked constrictions of the poles, a broad central area (relative to cell size) and 1 to 3 stigmata, that was never reported in South America. Conclusions: The studied populations correspond to D. geminata ssp. geminata Metzeltin & Lange-Bertalot. From a morphological point of view the smaller morphotype present in Santa Cruz belongs to the same subspecies but can be easily misidentified during the routine monitoring programs carried out with light microscope due its size and valve outline.