Different stains are used to internally mark calcified structures of mollusc shells in growth experiments. Because of interspecific variations in marking success, an assessment of suitability for each species is necessary. The potential of calcein, alizarin red, and strontium chloride hexahydrate (strontium chloride) was investigated for the Chilean abalone Concholepas concholepasr and the surf clam Mesodesma donacium, two molluscs of commercial importance in Chile. Wild specimens from Northern Chile were marked using different concentrations and immersion periods of the three stains. Animals were reared for 20 days to allow growth, mortality, body condition index (BCI), and growth rate was measured to assess the effects of the treatments. To detect marks, individuals were culled and shell sections analyzed using scanning electron microscopy for strontium chloride and fluorescence microscopy for calcein and alizarin red, respectively. Strontium chloride produced narrow bright bands only at concentrations of 2,880 mg·l⁻¹ and 24 h exposure. Calcein markings produced fluorescent bands detectable in all treatments (50 and 100 mg·l⁻¹, 3 and 6 h) whereas alizarin red only yielded irregular bands with 50–100 mg·l⁻¹ and 6 h exposure. Our results show that growth rates of C. concholepas are significantly affected by the stains factor: Strontium chloride showed the lowest growth rates whereas that of alizarin red and calcein was similar to the control group. High concentrations of strontium chloride negatively affected (P < 0.05) the body condition of the gastropod. Although no statistical differences were found, BCI of M. donacium followed the same trend as observed for C. concholepas. In conclusion, calcein was the best growth marker for both species because it produced bright, long-lasting bands even at low concentrations and immersion times without detectable lethal or sublethal effects.