The separate and combined effects of ammonium (10M) and phosphate (2M) on the ultrastructure of zooxanthellae (Symbiodinium sp.) from giant clams, Tridacna maxima, were examined in the field. Nitrogen addition significantly changed the ultrastructure of the zooxanthellae inhabiting the clams. After 9 mo exposure, the cross-sectional area of zooxanthellae from N-treated clams was significantly lower than that from other treatments [N=39.3 m²; C=47.9 m²; P=43.2m²; N+P=44.5 m²; (P=0.001)]. There was also a significant decrease in the size of starch bodies, especially around the pyrenoid of the zooxanthellae from N and N+P treatments [N=1.2 m²; C=2.0 m²; P=1.8 m²; N+P=1.2 m²; (P=2.08E-11)]. This presumably occurs as a result of the mobilization of organic carbon stores in response to stimulated amino acid synthesis under enriched nutrient conditions. These data strongly suggest that the symbiotic zooxanthellae of clams are limited to some extent by the availability of inorganic nitrogen, and that relatively minor changes to the nutrient loading of the water column can have substantial effects on the biochemistry of symbioses such as that which exists between clams and zooxanthellae.