The Critically Endangered Hooded Grebe Podiceps gallardoi has suffered a population decline of 80% since the 1980s. The evolutionary history and its critical conservation status place it 20th in the EDGE of Existence Bird List (EDGE-ZSL) among the more than 10,000 bird species of the world. The identification of demographically independent units (“management units”) is essential to address appropriate conservation and management strategies for threatened species. Genetic markers can be used to infer isolated populations without the need for logistically expensive banding and recapture. We used blood samples of 71 Hooded Grebes (c.10% of the global population) from three reproductive populations located at different plateaus that hold over 90% of the species’ global population. We analysed genetic population structure using a 353-bp fragment of mtDNA control region and 1,886 RAD loci to study whether Hooded Grebes are philopatric or not. We did not find differences in genetic structure of populations between plateaus indicating that Hooded Grebes do not consistently return to their plateau of origin. Our results are critical to understanding the connection of populations throughout the full annual movement cycle and propose management actions accordingly.