The early marine migratory behaviour of two populations of hatchery-reared Atlantic salmon Salmo salar was compared in a common-garden experiment. Post-smolts from a river in a long fjord (Lærdal River, 144 km from the open coastline, n = 79) and a short fjord (Flekke River, 20 km from the open coastline, n = 80) in western Norway were tagged with acoustic transmitters and released during the spring of 2005 and 2006 in the inner part of the Hardangerfjord system (Opo River mouth, 179 km from the open coastline). The migratory behaviour of the tagged fish was monitored by acoustic listening stations in the fjord system up to 167 km from the release site. The Lærdal fish began migrating before the Flekke fish and had higher progression rates in the middle part of the fjord system. A greater number of Lærdal fish was detected along the most direct migratory route and in the outermost part of the Hardangerfjord system, which is indicative of a higher survival. The results from this study demonstrate differences in early marine migratory behaviour between S. salar from two different stocks and suggest that the distance a S. salar population travels to reach the open coastline may influence its early marine migratory behaviour and performance. The selective pressures of marine predation and arrival time at feeding areas in the ocean may be stronger for stocks with a longer inshore migration, creating more efficient migrants over time.