Albatrosses attend fishing boats to feed on fishing discards but are often at risk of accidental bycatch. To examine whether populations (same species) and sexes differ in their overlap with fisheries due to differences in habitat use, we combined the use of recently developed loggers equipped with GPS and boat radar detectors with Automatic-Identification-System (AIS) data. Our study indicates that incubating wandering albatrosses (Diomedea exulans) from Crozet and Kerguelen foraged in different habitats although the duration of trips was similar. Both female and male Kerguelen birds took advantage of the large and productive surrounding shelf, whereas Crozet birds used the small shelf around the islands in a smaller extent. In Crozet, there was segregation between males and females, the latter favouring deeper and warmer waters. The two strategies of habitat use led to different overlap and attraction to boats, with Kerguelen birds encountering and attending boats for longer and at closer proximity to the colony than Crozet birds. Crozet females encountered boats at greater distances from the colony than males. Because of different habitat use, foraging outside EEZ and further to colony, Crozet birds attended more non-declared boats (without AIS) than Kerguelen birds. Albatrosses were more attracted by fisheries than cargo vessels and were especially attracted by fishing discards that led them to attend vessels for longer periods for both sexes and populations. The differences found between populations and individuals in terms of habitat specialization and encounter rate of fisheries should be considered for future assessments of risk of bycatch.