Many of the unionoid mussel species are threatened, and to be able to develop strategies for effective conservation, one of the needs is to distinguish host fish species from non-host fish species using reliable methods. Margaritifera margaritifera lives as a parasite on brown trout (Salmo trutta) and/or Atlantic salmon (Salmo solar). The aim was to compare the reliability of two methods measuring the host specificity of M. margaritifera in two rivers that flow out into Skagerrak in the Atlantic Ocean. A second aim was to compare the time- and cost-efficiency of the two methods. The methods were (1) natural encystment abundances on fish in their native streams using electrofishing, and (2) encystment abundances from controlled artificial infestation in aquaria, on fish that were sacrificed. In both rivers, young-of-the-year (YOY), but not older brown trout, were naturally infested with relatively low loads of glochidia larvae, while the Atlantic salmon was not infested at all. When using artificial infestation, both YOY and older brown had encysted glochidia larvae on their gills, while glochidia larvae were not able to develop in Atlantic salmon at all. Here, the encystment was higher on the brown trout from the Lade River, and older brown trout from the Lade River did not seem to have as strong immunity response compared to older brown trout from the Brattefors River. In summary, brown trout is the only host fish for M. margaritifera in these rivers. Both methods can be used to discriminate between host fish species, but the method measuring natural encystment seems most time- and cost-efficient. In addition, natural encystment can be measured using a non-destructive photo-method, and is therefore suggested to be used when discriminating between host fish species for M. margaritifera. (C) 2014 Elsevier GmbH. All rights reserved.