Members of the ammonium transporter family occur in all domains of life. However, they have been characterized, at the molecular level, mainly in bacteria and plants, whereas in animals their molecular characterization is limited to a few species. In marine invertebrates, recent studies have reported a multitude of physiological functions in which ammonium could take part. Among them, calcification is one for which very few data are available. In scleractinian corals, it has been reported that external sources of ammonium and/or ammonium containing compounds enhance calcification. However, despite these physiological insights, the underlying transport mechanisms are still unknown at the molecular level. In this study, we performed a first molecular characterization of ammonium transporters in the scleractinian coral Stylophora pistillata. By performing differential gene expression analysis, through quantitative real-time PCR, we show that S. pistillata ammonium transporters possess different tissue specificities. Most notably, one ammonium transporter, spiAMT1d, is specifically expressed in the coral tissue containing the calcifying cells. Furthermore, we determined spiAMT1d subcellular localization by immunostaining S. pistillata histological cross-sections and show that it localizes on the apical side of the calcifying cells and in their intracellular compartments. Taken together our results strongly suggest a role of ammonium transporters in coral calcification and lay the groundwork for many future studies aiming to better elucidate the potential role of ammonium in calcification.