This study describes chemical ecology investigations of predator-prey relationships in New Zealand nudibranchs for the discovery of new natural products. Three predator-prey relationships were established, and twenty secondary metabolites were isolated and characterised from various New Zealand marine organisms, including five new compounds. Predator-prey relationships were established for three nudibranch species, Polycera hedgpethi, Ceratosoma amoenum and Goniobranchus aureomarginatus by means of field studies and laboratory-based feeding-choice experiments. Results indicated that P. hedgpethi prefers the bryozoan Bugula neritina, while C. amoenum and G. aureomarginatus prefer feeding on the marine sponges Dysidea teawnui and Dictyodendrilla cf. dendyi, respectively. For two of the predator-prey relationships, common metabolites were found in both predator and prey. As such, Dysidea teawanui and C. amoenum both contain a sterol peroxide, while G. aureomarginatus and D. cf. dendyi both contain dictyodendrins C (209) and F (212). P. hedgpethi and B. neritina specimens were also chemically investigated but common metabolites were not found. Additionally, three nudibranch species, Dendrodoris krusensternii, Dendrodoris nigra and Aphelodoris luctuosa, were chemically investigated and yielded a range of secondary metabolites previously reported from marine invertebrates. A polymeric 3-alkyl pyridinium salt (146) was found in high concentration within A. luctuosa and its eggs. Moreover, an endemic bryozoan, Amathia gracei, was chemically investigated and yielded a known brominated alkaloid. Investigation of G. aureomarginatus samples by LC-MS screening, to determine metabolite distribution and any ecological role of the compounds isolated, indicated that dictyodendrins C (209) and F (212) were present in the digestive glands, while a norditerpene, gracilin was only present in the mantle. Quantitative NMR spectroscopy indicated that the polymeric 3-alkyl pyridinium salt (146) was present in higher concentration in the mantle of Aphelodoris luctuosa, consistent with a defensive purpose and with its presence in high concentration within the egg masses of A. luctuosa. Morphological analysis revealed oxea spicules within the digestive gland of Aphelodoris luctuosa, suggesting that it is possibly feeding on haplosclerid sponges. An additional seven known polyaromatic alkaloids and five new sulphated denigrins alkaloids, denigrins H-L (262-266) were isolated and characterised from the sponge D. cf. dendyi by means of NMR spectroscopy and HR-ESI-MS guided isolation. The new and known metabolites isolated in this research were assessed in a general cytotoxicity assay against HeLa cells. Results indicated that the compounds were not particularly active (IC50 > 57 µM).