Due to their strong antiseptic properties, silver nanoparticles (AgNPs) are widely used in consumer products, and therefore there is a high risk of their release to the aquatic environment. In the present study, we investigated chronic effect of waterborne AgNPs on the mRNA expression of four important biomarker genes including metallothionein (MT), glutathione S-transferase (GST), superoxide dismutase (SOD), and glutathione peroxidase (GPX) in the gill tissue of rainbow trout. Twenty-one-day exposure to AgNPs significantly increased MT and GST mRNA levels in the gills in a dose-dependent manner. Although mRNA levels of SOD significantly increased in the gills of fish exposed to AgNPs, but its increase was not dose-dependent. In contrast, exposure to AgNPs significantly decreased GPX mRNA levels in the gills. The results suggest that exposure to AgNPs can significantly change the expression of biomarker genes mRNA in rainbow trout.