The aim of the research was to explore the contribution of hepatic cytochrome CYP1A and metallothionein (MT) mRNA expression to biological effect monitoring. The study was conducted in the European flounder (Platichthys flesus) from the Gulf of Gdańsk. mRNA abundance was measured using reverse transcriptase polymerase chain reaction (RT-PCR) in liver RNA of fish sampled from three coastal stations and from one offshore station in the inner Gulf. The contribution of the mRNA-based biomarkers to the assessment of the environment was determined in conjunction with a selection of commonly applied biochemical markers: 7-ethoxyresorufin-O-deethylase (EROD), glutathione-S-transferase (GST), catalase (CAT), metallothioneins (MT), fluorescent aromatic compounds (FACs), all measured in the same individual fish. The mRNA biomarkers contributed to the separation between the sampling sites, but no correlations between CYP1A mRNA and EROD nor between MT mRNA and MT proteins were found, which should be attributed to the different levels these biomarkers correspond to and to the differences in factors that may affect them. One case of strong correlation between CYP1A mRNA and FACs was encountered. The overall results of this study suggest that biomarkers measured at the mRNA abundance level constitute a valuable addition to biomonitoring studies by providing additional information and contributing to the differentiation of results.