Coral reefs are a critical resource to developing and developed nations world wide. Providing shelter, food, monetary value, and a vast resource of ecological wealth, the corals of the reefs underpin an entire ecosystem. Climate change, driven by increased greenhouse gases, is raising the temperature of Earth’s waters and atmosphere, while making the planet’s oceans increasingly acidic. Brightly lit and increasingly warm tropical waters present a potentially challenging environment in which scleractinian corals grow. In attempting to cope with the competing stresses of intense photon flux density (PFD) and anomalously high sea surface temperatures, corals and dinoflagellates exhibit myriad biochemical and physiological adaptations. Pocilloporins, a diverse group of non-fluorescent green fluorescent protein (GFP) homologs found across Cnidaria and beyond, are one such adaptation within the tissues of heavily pigmented scleractinian corals. Chemically unique amongst pigments, GFP-like pigments exist as pure protein chromophores and exhibit little to no cytotoxicity when naturally occurring. This non-fluorescent class of GFP-like pigments has found popularity in biochemical and biotechnological applications, though an ecological and evolutionary explanation for the heavy conservation of pocilloporins across a broad range of scleractinian corals and related cnidaria is still a subject of scientific research and debate. This thesis supports the hypothesis that pocilloporins act as a naturally occurring photoprotective pigment in reef-building corals, specifically acting to filter and regulate the light environment within coral polyps. In examining the role of pocilloporins in Scleractinia, the need to examine environmental sources of pigment production induction and suppression, the localization of pigments within coral tissues and cells, and the ability of coral colonies to direct resource allocation with regards to pocilloporin production were identified as lines of inquiry. Briefly, for experiments examining either pocilloporin induction or suppression, the following aspects were studied: holobiont responses in the form of mRNA signal expression, host pigment isolation and analysis, dinoflagellate density and pigmentation sampling, and chlorophyll fluorescence of live corals. Blue morph Acropora aspera, common to the reef flat of Heron Island (Great Barrier Reef, Australia), were subjected to 99% shade and thermal bleaching threshold temperatures in separate attempts to suppress pocilloporin expression, while red morph Montipora monasteriata was transplanted at equivalent depth from their natural cave environments to exposed portions of the spur and groove formations of the northern face of Wistari Reef (Great Barrier Reef, Australia). Both ambient temperature and heat-stressed A. aspera were concurrently collected during the thermal stress experiment and placed in preservatives for immuno-histochemical localization of pocilloporins with their tissues. Finally, radio-labelled glycine, a very common amino acid in the primary sequence of pocilloporin, was injected into artificially injured tan morph Montipora monasteriata, also on the northern face of Wistrai Reef to study the uptake of dissolved organic materials (DOM) and incorporation of metabolic resources into newly generated pigments. Pocilloporins proved easier to induce in this work than suppress, and the location of these pigments in A. aspera tissues suggests a potential mechanism. The data demonstrated the presence of pocilloporins in the most directly exposed epidermal and gastrodermal tissues of the coral polyp, specifically the outermost layers of epidermis and gastrodermal layers bordering directly upon the gastrovascular cavity. Closer inspection through anti-pocilloporin-gold stained TEM images was highly suggestive of pocilloporin secretion in coral mucus, a theory separately supported by observations of coral mucus in collected live corals. Neither suppression experiment induced heavy mucus sloughing in A. aspera, so despite multi-fold reductions in pocilloporin mRNA as a result of applied stimuli, the continued presence of pocilloporin aaCP592 in blue morph A. aspera is not surprising. Conversely, pocilloporin msCP576 in plating Montipora monasteriata was induced in response to both general increases in PFD and specific increases of PFD at the sites of physical injury. Additionally, tan morph Montipora monasteriata demonstrated the capacity to collect and allocate DOM from the environment to assist in the production of new pigments and tissues, an energetically expensive process. The reduction of the orange-red spectrum in favour of the blue light ranges is generally beneficial to the photosynthetic systems of both higher plants and the resident dinoflagellates of corals. msCP576 and aa592, both positively identified as pocilloporins within this work, absorb within the orange-red region and apparently act as a photoprotective filter in all exposed surfaces of heavily pigmented corals, enhancing the blue spectrum of incident and reflected PFD and generally regulating the internal light environment.