Nitrogen is a vital nutrient for all organisms forming an integral part of DNA, RNA and amino acids. Highly productive coral reef ecosystems form in the nutrient poor waters of the tropics. As such they are adapted to low nitrogen concentrations and have been observed to experience negative effects when levels increase. Developing our knowledge of how coral and their symbiotic dinoflagellates, Symbiodinium, respond to changing exogenous nitrogen concentrations, on both a physiological and genetic level, will help in understanding why coral respond to increases in nitrogen and provide a basis for management decisions to preserve these essential environments. This thesis examined the effects of elevated ammonium and nitrate on the physiology of the coral host, Acropora aspera, and its symbiont, Symbiodinium sp.. Additionally, the genes involved in ammonium and nitrate uptake and assimilation were identified, and expression changes were examined. Both ammonium and nitrate are depleted from seawater at greater rates in the light than when incubated in darkness. The addition of glucose can recover the uptake of nitrate in the dark and even enhance light uptake, however the uptake of ammonium remains unaffected by glucose additions. It is speculated that the failure of glucose to recover dark ammonium uptake is related to coral carbon stores; when carbon stores are high, assimilation can occur in darkness, conversely when they are depleted assimilation can no longer occur as the carbon skeleton stores have been exhausted. Comparatively, nitrate assimilation is more energy costly and is thus dependent on a more direct energy source that can be supplied in the form of glucose. Once ammonium has been acquired by the coral symbiosis, both the coral host and its symbiont are able to assimilate it. However, Symbiodinium are able to assimilate 14 to 23 times more ammonium than their coral cell counterparts. Symbiodinium retain their assimilated products for 11 hours before some is released back to the host. Elevated levels of both ammonium (20 μM) and nitrate (10 μM) lead to physiological changes in both the coral host and its symbiont, with commensurate increases in the amino acid and protein pools. Additionally Symbiodinium experienced increases in Chlorophyll a pigments as well as an increase in population density. Many genes are involved in the acquisition and assimilation nitrogen. Three ammonium transporters (SyAt1, SyAt2 and SyAt3), one nitrate transporter (SyNt) and a glutamate synthase (SyGOGAT) gene were identified and their sequences examined. Phylogenetic analysis showed the ammonium transporters (AMT) came from two different AMT families, the plant–like AMT2 family and the bacterial like AMT1. Nitrate Transporter (NAT) SyNt originated from a red algal lineage whilst SyGOGAT branches as an out-group to all other organisms included. These diverse lineages highlight the diversity of lineages contained within the dinoflagellate genome. The addition of ammonium and nitrate over a period of 12 days resulted in increases in the expression profile of all genes examined. These increases would allow the coral holobiont to maximise the acquisition and assimilation of nitrogen during a pulse event. The results of this study show that both the coral host and its symbiotic dinoflagellate experience physiological changes to varying exogenous nitrogen concentrations. These physiological changes are underpinned by genetic changes in Symbiodinium and predictably in coral as well.