Accurate estimations of adult mortality are essential for understanding population dynamics and achieving efficient management actions that are directed toward long-lived species. Several noninvasive methods may be used to monitor endangered long-lived birds like raptors, but their performance in real-world scenarios remains poorly studied. We used eight Bonelli's Eagle (Aquila fasciata) breeding pairs (1) to compare the efficiency of direct observations with binoculars and telescopes (2004–2016), camera trapping (2012–2016), and feather genetic analysis (2004–2015) for detecting and identifying individuals over time, (2) to conduct a cost-benefit analysis of methods, and (3) to evaluate the accuracy of the direct observation method for estimating survival by comparing it with camera trapping and feather analysis. Both the feather genetic analysis and camera trapping approaches allowed us to successfully identify individuals and to detect replacements that we did not notice during direct observations. The classic direct observation method overestimated adult survival, which could hamper an accurate understanding of the demographic dynamics of this population. Feather analysis gave a low detection rate of individuals (47%), probably due to difficulties in finding feathers in the rugged habitat of this species. However, identification success at the individual level with this method was 96%. Remote camera surveys had both a high detection rate (100%) and identification success (93%). Given that costs associated with camera surveys were lower than the costs of genetic procedures, we concluded that camera trapping is the most efficient indirect method to assess adult survival in this and other raptors with external features that make individual identification possible. However, because no method showed complete efficiency, genotyping of feathers collected at the end of the breeding season could be a useful additional method, especially when camera trapping is not possible or when it fails.

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