The worldwide growth of the marine aquarium market has contributed to the degradation of coral reef ecosystems. Enforcing the legislation on importing ornamental species has led some European traders to concentrate on local species. Portugal is used as a case study of marine ornamental fish and invertebrate collection in European waters. One hundred and seventy two species occurring in Portuguese waters (mainland, the Azores and Madeira archipelagos) were considered as potential targets for the marine aquarium industry, some of which are already traded on a regular basis (e.g. Clibanarius erythropus, Lysmata seticaudata, Cerithium vulgatum, Hinia reticulata and Ophioderma longicauda). To ensure appropriate management and conservation of these resources, the following options have been evaluated: banning the harvest and trade of all marine ornamental species from European waters; creating sanctuaries and “no take zones”; issuing collection permits; creating certified wholesalers; implementing the use of suitable gear and collecting methods; setting minimum and maximum size limits; establishing species-based quotas; protecting rare, or “key stone” species and organisms with poor survivability in captivity; establishing closed seasons; culturing ornamental organisms; and creating an “eco-fee” to support research and management. Establishing this sustainable alternative fishery may help minimise the economical and social impacts caused by the crash of important food fisheries in Portugal and other European and West African countries.