Selenium is an essential trace element for humans and animals. Fish and shellfish are known to be rich in selenium and suppose to be an effective selenium source. In this study, we characterized the selenium species in the Shijimi clam ( Corbicula japonica ), which is a typical clam eaten in Japan. The Shijimi clam contains a relatively high concentration of selenium (3.5 µg-selenium/g-dry Shijimi). Approximately 30% of the total selenium in the Shijimi clam meat was extractable with water, while selenium in the Shijimi clam was hardly extracted with ethanol, chloroform and hexane. Based on an ultrafiltration study, the molecular mass of the major selenium species in the Shijimi water-extract was estimated to be less than 5000. Because amphoteric selenium species were contained in the Shijimi water-extract, which was indicated by ion-exchange chromatographic separation, an ion-pair reagent was utilized to extract the ionic selenium species into an organic solvent. A matrix assisted laser desorption ionization (MALDI) time of flight (TOF)-mass spectrometric analysis revealed the selenium isotopic pattern involving one selenium atom in a molecule with the ⁸⁰Se molecular ion peak at m / z 534. This selenium species was mainly found in the visceral part of the Shijimi clam by imaging mass spectrometry.