A new instrument designed for in situ chemical marking experiments was developed and applied to the deep-sea seep clams Calyptogena soyoae and Calyptogena okutanii. Fluorochrome calcein was used for vital staining of four living clams kept in a specially designed in situ growth chamber that was placed on the seafloor at a cold-seep site off Hatsushima Island, Sagami Bay, central Japan. The shell margins of both C. soyoae and C. okutanii were clearly stained, forming a thin fluorescent band. This method will be useful for age and growth-rate determinations of many other marine organisms with accretionary growing skeletons.