Colour is a remarkable feature among animals and it has diverse roles including camouflage, signalling, and photoprotection, all of which impact survival and reproduction. Moreover, colour is not always a fixed feature and can vary within a species, either between individuals or throughout an individual’s life, and is generated by nanostructures and/or pigments. Animal pigments can be synthesised or acquired through diet, with common pigment classes including carotenoids, tetrapyrroles and melanins. Research on pigments has gained momentum due to their numerous scientific and industrial applications. For instance, the green fluorescent protein (GFP), a fluorescent marker first identified in the jellyfish Aequorea victoria, is widely used in biomedical research. Despite the intense scientific interest in GFPs, little is known about the phylogenetic distribution and function of jellyfish pigments. Catostylus mosaicus, for instance, a rhizostome jellyfish that occurs abundantly in eastern Australia, can exhibit striking colour variation: it can be blue, white, or brown, and may also feature a blue band around the bell and/or oral arm proximal margins. However, the pigments responsible for these colours and the underlying drivers of colour variation are unknown. Therefore, the main objective of this thesis was to integrate chemical and genetic analyses to investigate colour variation in Catostylus mosaicus. [...]