In this study a time- and cost effective method for marking early life stages of brown trout (Salmo trutta L.) with alizarin red S (ARS) is presented. The main intention was the development of a protocol to mark embryos. When stocking eyed-eggs, later recognition depends on an adequate tagging method featuring reasonable expenditures, low mortality and high marking success. Best results were obtained using ARS concentrations of 500 mg/l. Consistently clearly visible marks could be detected under a fluorescence-stereomicroscope equipped with a dsRed filter, without processing the otoliths.