Sea ranching of the saucer scallop Amusium balloti Bernardi, 1861 has recently been developed to compensate for the dramatic fluctuations in catch that naturally occur between seasons. Marking or tagging methodology is needed for this industry to evaluate the effectiveness of reseeding and to optimize spat deployment strategies. We tested the quality and longevity of fluorescent marks incorporated into the newly forming shell of 2–4 mm spat immersed in chemical solutions. Three chemicals, alizarin red S (ARS), calcein, and oxytetracycline hydrochloride (OTC) were tested in this study for mark quality, mark retention, and toxicity to scallops. Marks were identified and assessed for brightness using an epifluorescence microscope. Fluorescent marks were still visible after 10 mo of culture in our land-based system. Multiple marks were also produced on individual shells using OTC or a combination of calcein and OTC. This demonstrates the potential for specific “bar codes” to be used to distinguish between different cohorts or spat deployment strategies. Of the three chemicals, OTC was identified as the most useful chemical for industry, producing a bright mark and negligible mortality at 200 or 300 mg L⁻¹, which lasts for at least 10 mo in living scallops.