Giant clams harbor symbiotic zooxanthellae (Symbiodinium)， which are nitrogen-deficient， mainly in the fleshy and colorful outer mantle. This study aimed to sequence and characterize the algal Glutamine Synthetase (GS) and Glutamate Synthase (GLT)， which constitute the glutamate synthase cycle (or GS-GOGAT cycle， whereby GOGAT is the protein acronym of GLT) of nitrogen assimilation， from the outer mantle of the fluted giant clam， Tridacna squamosa. We had identified a novel GS-like cDNA coding sequence of 2325?bp， and named it as T. squamosa Symbiodinium GS1 (TSSGS1). The deduced TSSGS1 sequence had 774 amino acids with a molecular mass of 85?kDa， and displayed the characteristics of GS1 and Nucleotide Diphosphate Kinase. The cDNA coding sequence of the algal GLT， named as T. squamosa Symbiodinium GLT (TSSGLT)， comprised 6399?bp， encoding a protein of 2133 amino acids and 232.4?kDa. The zooxanthellal origin of TSSGS1 and TSSGOGAT was confirmed by sequence comparison and phylogenetic analyses. Indeed， TSSGS1 and TSSGOGAT were expressed predominately in the outer mantle， which contained the majority of the zooxanthellae. Immunofluorescence microscopy confirmed the expression of TSSGS1 and TSSGOGAT in the cytoplasm and the plastids， respectively， of the zooxanthellae in the outer mantle. It can be concluded that the symbiotic zooxanthellae of T. squamosa possesses a glutamate synthase (TSSGS1-TSSGOGAT) cycle that can assimilate endogenous ammonia produced by the host clam into glutamate， which can act as a substrate for amino acid syntheses. Thus， our results provide insights into why intact giant clam-zooxanthellae associations do not excrete ammonia under normal circumstances.