Cyanobacterial blooms are commonly associated with high concentrations of nutrients in waters. An exception among the species forming heavy water blooms is Limnoraphis robusta Komárek et al. (Fottea 13:39–52, 2013). Until now, heavy water blooms of this species were found only in tropical, rather oligotrophic waters. Filaments of L. robusta contain diazocytes and thus are able to fix molecular nitrogen during night. This ability gives L. robusta an advantage over other phytoplankters to explore nitrogen-poor habitats. In 2014, filaments of this cyanobacterium appeared also in plankton and peri-phyton in the Bay of Puno, Lake Titicaca, Peru. Accessible data on water chemistry, chlorophyll a concentration, and phytoplankton composition were compared with those from Lake Atitlán, Guatemala, where this cyanobacterium formed a thick brownish layer on the water surface in 2008, 2009 and 2011. Except for shallow bays, both lakes (Atitlán and Lago Mayor of Titicaca) are still oligotrophic in some periods, and phytoplankton growth is limited by lack of nitrogen. In this paper, we are discussing factors which might allow development of heavy bloom of this cyanobacterium in the Lago Mayor and other clear parts of the Lake Titicaca.