Brown trout (Salmo trutta L. 1758) and Arctic charr [Salvelinus alpinus (L. 1758)] tagged with acoustic transmitters migrated from fresh water to the sea mainly in May and June, but with large individual variation in migration timing. For S. trutta, large individuals (42–86 cm total length) migrated earlier in the season than small individuals (18–27 cm). For S. alpinus, no such pattern was found, likely because of the small size range of tagged fish (28–41 cm). S. trutta stayed longer at sea than S. alpinus (average 2 vs. 1 month). Early migrants of S. trutta stayed for a shorter period at sea than late migrants, whereas no such pattern was observed for S. alpinus. Large S. trutta moved quickly away from the river and spent average 3 days to reach a receiver line 20 km from the river mouth, whereas small S. trutta and S. alpinus migrating that far spent 2–3 weeks on the same distance. S. trutta utilized the entire fjord system and had a greater proportion of long-distance migrants (>20 km, 78% and 59% of large and small S. trutta, respectively) than S. alpinus (29%). S. alpinus mostly stayed in the inner fjord areas, and none were recorded in the outermost part of the fjord. The difference in the use of marine areas may be caused by variation in prey choice and spatial distribution of the preferred prey groups. Stable isotope analysis showed that S. trutta had been feeding at a higher trophic level than S. alpinus. S. trutta had mainly fed on marine fish and shrimps, whereas S. alpinus had large proportions of freshwater invertebrates in the diet, suggesting that the estuary with benthos and amphipods drifting from the river was an important feeding habitat for S. alpinus. In conclusion, major differences in habitat use, migration patterns and feeding strategies were found between sympatric anadromous S. trutta and S. alpinus while at sea.