Rivers draining into (Lake) Inarijärvi, northern Finland, sustain a number of lake-run brown trout, Salmo trutta, populations but, as with most lake-run S. trutta systems, the level of population genetic structuring among populations is unknown. To address this and to assist fish stock management in the region, the population genetic structure of S. trutta collected from 28 sampling sites in rivers flowing into Inarijärvi was studied using 13 microsatellite loci. Populations were clustered into three separate groups, largely corresponding to geographic regions, with between-region FST values ranging from 0·11 to 0·16. The significant differentiation observed between most populations within each region also implies that individual populations should be recognized as separate management units and actions to improve, and subsequently maintain, conditions for natural spawning should be prioritized. The results of this study further indicate that the trout from each of these regions may have different biological characteristics, such as local-lake feeding behaviour among the western populations and strong isolation among the northern stocks. As a consequence, further research is warranted to better understand the level of ecological uniqueness of lake-run S. trutta populations.
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