Plant oil utilization in aquafeeds is still the most practical option, although it decreases the content of the nutritionally highly valuable omega-3 fatty acids eicosapentaenoic acid (20:5n-3, EPA) and docosahexaenoic acid (22:6n-3, DHA) in fish. Phytoestrogens and their metabolites are putatively able to affect genes encoding proteins centrally involved in the biosynthesis of EPA and DHA due to their estrogenic potential. Thus, the aim of the study was to screen the potential of the phytoestrogens to stimulate the biosynthesis of EPA and DHA in rainbow trout (Oncorhynchus mykiss). Additionally, the potential effects on growth performance, nutrient composition and hepatic lipid metabolism in rainbow trout were investigated. For that, a vegetable oil based diet served as a control diet (C) and was supplemented with 15 g/kg dry matter of biochanin A (BA), daidzein (DA), genistein (G) and equol (EQ), respectively. These five diets were fed to rainbow trout (initial body weight 83.3 ± 0.4 g) for 52 days. Growth performance and nutrient composition of whole body homogenates were not affected by the dietary treatments. Furthermore, feeding EQ to rainbow trout significantly increased DHA levels by +8% in whole body homogenates compared to samples of fish fed the diet C. A tendency towards increased DHA levels in whole body homogenates was found for fish fed the diet G. Fish fed diets BA and DA lacked these effects. Moreover, EQ and G fed fish showed significantly decreased hepatic mRNA steady state levels for fatty acyl desaturase 2a (delta-6) (fads2a(d6)). In contrast, carnitine palmitoyl transferases 1 (cpt1) hepatic mRNA steady state levels and hepatic Fads2a(d6) protein contents were not affected by the dietary treatment. In conclusion, when combined with dietary vegetable oils, equol and genistein seem to stimulate the biosynthesis of DHA and thereby increase tissue DHA levels in rainbow trout, however, only to a moderate extent.