Population growth of piscivorous species raises concerns when it could affect aquaculture activities. In this study, an increase of the Neotropic Cormorant (Phalacrocorax brasilianus) population in the Ecuadorian Andes was documented using census data from three high Andean lakes (Yahuarcocha, San Pablo and Yambo) for 2004–2010. In the 20th Century, only one record of the species existed for the study area. From 2005 onward, the species occurred regularly at all three lakes. At Yahuarcocha, the wintering population (October–February) grew at an annual rate of 0.382 ± 0.05, reaching 307 in 2010. The population consists mainly of non-breeding migrants, and at the present time, the wintering distribution range of cormorant populations in Ecuador includes the high Andes. Given reports of cormorant predation at fish farms, potential conflicts on account of cormorant expansion are discussed.