There are six species of flamingos in the world, all under pressure from human activities in their wetland habitats. Obtaining global population estimates for flamingos is challenging because of their broad geographical range, nomadic movements, capacity for long-distance flight, and the complexity of international monitoring. Two species, the Andean Flamingo Phoenicoparrus andinus and Puna Flamingo P. jamesi, during key parts of their life cycle, use wetlands in the Andes of South America, where they coexist at various sites. We compiled historical information on population estimates and ecology for these two species and integrated data collected on regional simultaneous censuses to describe population trends, current and emerging threats, and provide recommendations for conservation action. Long-term population trends have been difficult to establish given the unreliability of population estimates prior to the late 1990s. Systematic, regional censuses carried out regularly since 1997 have produced robust population estimates for the Andean and Puna flamingos (most recently, 78,000 and 154,000, respectively) and show populations of both species to be stable and increasing. Increasingly rapid changes in wetlands caused by human activities such as industrial-scale mining in breeding and foraging sites in the high Andes wetlands, and agro-industrial activities in their lowland wintering sites, focused on areas of the highest concentrations of flamingos pose threats to their survival and ability to reproduce. In addition, climate change is projected to reduce wetland habitats and some localised effects have already been detected. Continued research on the ecological drivers of flamingo abundance, movements, and population genetics to understand population structure and dynamics are necessary, as well as the identification of response variables to changing environmental conditions. Interdisciplinary and systems-level approaches in the context of international collaboration in monitoring and conservation planning among a diversity of stakeholders will be required to safeguard flamingo populations and wetland habitats.