This paper is a panoramic, though incomplete, review of the Peruvian marine biodiversity, including the Peruvian coastal upwelling ecosystem, the marine shallow areas of the Peruvian coast and the mangrove ecosystem of the north of Peru. It includes an analysis of the advances in conservation and management, as well as of research resources. The analysis mainly showed the insufficient human resources and the limited facilities in laboratories and coastal research stations. An analysis was also made from the current unknowns of the research at taxonomy and ecosystem levels, indicating scarce studies for most of the taxonomic groups and biological communities. Finally, the consultations and discussions promoted with the scientific community, allowed the identification of the following issues as the main challenges for future research: formation and training of human resources, development of inventories, studies on endemism and speciation areas, application of new technologies for monitoring physical and biological parameters of the ecosystem, and assessment of the impacts of climate change on marine biodiversity.