Chemical prospecting for pharmaceuticals in natural organisms (bioprospecting) has been both championed as a tool for conservation and criticised for not being environmentally sustainable. However, there has been little attempt to address the ways that bioprospecting could contribute to conservation if undertaken in an ecologically sustainable manner. Bioprospecting can provide financial benefits, but these are unlikely to advance natural resource management unless contractual agreements granting access to biodiversity specify that a percent of the fees and royalties must be used to fund conservation projects. A more likely positive outcome for conservation is that bioprospecting provides funding opportunities for the rapid documentation of biological diversity. If representative specimens of each sampled taxa are lodged in accredited institutes, a useful resource will be available for other research projects. Bioprospectors can also emphasize the need for conservation by increasing the community's appreciation for marine biodiversity. Nevertheless, bioprospecting will only be compatible with conservation objectives if it can be shown to have no negative impacts on the environment. There is some evidence that marine organisms have been over-collected for natural products research, although it is currently difficult to assess the impacts of marine bioprospecting due to the fact that the sample quantity and abundance of the target organism are rarely published in the scientific literature. It is apparent that research on the natural history and ecology of target organisms needs to be assigned greater priority. Bioprospecting could be undertaken with minimal impact on abundant species with broad geographic distributions because modern technologies permit the preliminary identification of bioactive compounds from small samples (<100g). However, environmental impact assessment may be necessary for the recollection of organisms prior to complete chemical characterisation and pharmacological evaluation. Once a useful compound has been identified several options are available for large-scale production, including chemical synthesis and aquaculture. By adopting a precautionary approach, new marine bioresources could be developed in a sustainable manner. Consequently, bioprospecting does have potential to contribute biodiversity research and the conservation of natural resources.