Metabolism of xenobiotics is a two-step process that increases the polarity of compounds to facilitate their excretion. In previous work, the major in vitro phase I metabolites of alkyl-anthracenes by rainbow trout (Oncorhynchus mykiss) CYP enzymes were shown to be predominantly ring hydroxylated metabolites. Here, we present the first report on the identification of in vivo phase II metabolites of alkyl-anthracenes in juvenile rainbow trout. Bile was collected from trout injected with individual alkyl-anthracenes with, in some cases, a co-injection of β-naphthoflavone (BNF). Some samples were digested with the β-glucuronidase enzyme to confirm the presence of glucuronide conjugates. The metabolites were separated using a water–acetonitrile gradient on a HPLC system equipped with a C18 column and a UV-diode array detector. Trout with endogenous and BNF-induced enzymes produced the same metabolites, but higher concentrations of metabolites were detected after enzyme induction. Alkyl-anthracenes were metabolized predominantly on the rings as evidenced by the UV spectral analysis. Likewise, mass spectrometry and UV spectral analysis confirmed a predominance of glucuronide conjugates for all systems investigated.