The cyanobacteria Cylindrospermopsis raciborskii, is a fresh water ubiquitous species from tropical to temperate weather. It is potentially capable of producing toxins.  Thus it is necessary to monitor its presence in fresh waters associated to recreational use activities and human consumption. There are official reports and one thesis reporting the presence of C. raciborskii in Ecuador. Nevertheless, this country does not appear in the latest distribution maps of this species in the scientific literature. In this article, we report the presence of C. raciborskii in Ecuador, together with the characterization of the environmental conditions of one of the habitats where this species is present: the Limoncocha lagoon, province of Sucumbíos.