The marine biodiversity of Gokova specially protected area (SPA) lead a serious contradiction between conservation of biodiversity and human use. Among 723 macroscopic species, Gokova SPA sheltered 34 species under protection. However, possible solutions have been proposed to the authorities for the problems recorded during this study. Problems related to over fishing, anchoring, wastewater reclamation, the yacht tourism and aquaculture needs immediate attention and some progress to solve these problems has already been achieved. The further measures should include other threats on the biodiversity such as the selective fishing, trading of protected species and habitat loss due to land use. Solutions on scientific basis should be developed in order to conserve the marine biodiversity as well as a sustainable fisheries and ecotourism in specially protected areas and Gokova Spa is a promising example for such attempts.