In many seabird species, the genetic structure of the populations remains poorly known despite potential consequences for conservation. The globally threatened wandering albatross Diomedea exulans displays specific traits, including limited population size, strong philopatry, adults almost always returning to breed on the island where they made their first breeding attempt, delayed maturity, high longevity and low fecundity. Using both genetic and demographic methods, we evaluated how these traits might affect the structure within (inbreeding, low variability) and among (restricted gene flow) discrete wandering albatross colonies. Our study was conducted on Possession Island, Crozet archipelago, and in the Kerguelen archipelago. The genetic approach was based on three colonies and 10 microsatellite loci. The demographic approach used data from a 36-year capture–mark–recapture survey of the entire population from Possession Island. Inbreeding occurred as often as expected under random pairing. Genetic variability in each colony did not exceed 6.3 alleles per locus. However, no genetic bottleneck was detected. No significant genetic differentiation occurred between the two main colonies from Possession Island (Fst<0.01), consistent with our demographic estimates of dispersal. Conversely, the genetic differentiation between Possession Island and Kerguelen was significant. Although males are more philopatric than females, genetic differentiation among colonies was not higher in males and no significant genetic differentiation between sexes was observed. Finally, we propose that the population from Crozet and that from Kerguelen are considered as distinct management units.