Alizarin red S from 200 to 5000 mg L )1 was used to mark the otoliths of whitefish embryos Coregonus lavaretus (L.) from 5 days after fertilization until shortly before hatching, to develop a method for evaluating the effect of stocking whitefish. Mark quality depended on developmental stage at the time of immersion. The best results were obtained when the otolith primordia had formed and had started aggregating to form the innermost part of the nucleus. This was verified by in vitro staining of otoliths where the primordia were more intensely stained than the remaining part of the nucleus. The volume ratio eggs to ARS solution, which was 1:10 in all but two treatments, must be observed when comparing fluorochrome concentrations, as mark quality decreased at higher ratios of 1:5 and 1:2. An average mortality rate of 35% in the most successful treatments was considered tolerable for a mass-marking programme being used under commercial hatchery conditions. This method for marking otoliths of whitefish embryos with ARS during egg incubation is recommended for all cases where marking of larvae is not possible.K E Y W O R D S : alizarin, Coregonus, otolith marking, otolith primordia, whitefish.