Conservation efforts for large raptors require robust estimates of fecundity, age at maturity and survivorship, and population trajectories are often particularly sensitive to change in adult survival rates. Our study estimated apparent survival rates in territorial range-holding Golden Eagles Aquila chrysaetos in Scotland, based on DNA extracted from moulted feathers to profile individuals genetically: the first study for this species using the method. Feathers were collected at or close to nest sites within 93 home ranges involving 136 territorial individuals, across four years (2006-2009), with repeat-sampling in 21 % of home ranges. Genetic profiles identifying individuals’ presence/absence were analysed to estimate annual apparent survival rates using Cormack-Jolly-Seber models. Our models included sex, as male survival was expected to be lower, and two regions, the Outer Hebrides and the Inner Hebrides/Highlands, that host largely separate sub-populations. Estimates of male annual apparent survival rates (0.774-0.808) were markedly lower than females in both regions (0.878-0.882), but encounter rates of males (0.441-0.454) were also lower than females (0.639-0.754), probably because males spend less time near nest sites. We recorded a few instances of breeding dispersal, mostly involving females moving to neighbouring territories. Our estimates of apparent survival were probably close to true natural survival but possibly reduced by some illegal killing in the Inner Hebrides/Highlands. Annual rates for females were similar to previous estimates derived for the same age/status class which utilised other methods but did not separate the sexes. The different field methods used to estimate large raptor survival have advantages and disadvantages. Genetic profiling allows survival estimation of territorial occupants, but its sampling focus around the nest site creates limits in applicability. In our study system, where eagles may be killed illegally before providing opportunities for feather collection, genetic profiling is poor for detection of persecution mortality, and GPS-tagging is better.