Understanding the relative contributions of potential source populations to fishery catches is vital for proper management of harvested fish stocks. Little is known about the temporal variation in commercially important brown trout (Salmo trutta) catch in large boreal lakes. We estimated contributions of 34 putative source populations to the brown trout catch in two lakes, Inarijarvi and adjacent Paadarjarvi (northern Finland) during 2006-2011. Genetic stock identification indicated that there is considerable temporal variation in the catch proportions in Inarijarvi and they are mainly associated with different contributions of the tributaries of the Ivalojoki and Juutuanjoki. In Paadarjarvi, catch proportions were relatively constant during the sampling period. Our study demonstrated the importance of temporal sampling when estimating catch proportions for management purposes.