The Southeastern Pacific Ocean is characterized by a large diversity of marine living resources with a high demand in world markets. Deep-water species such as the Patagonian toothfish Dissostichus eleginoides are among the most important marine resources in this region. Peru has a Patagonian toothfish fishery dating back 15 years, with relevant international markets for exportation. However, similar that others countries in the region, Peru has poor scientific data for stock assessment of this species. Furthermore, the current monitoring program of this fishery does not provide an adequate control of onboard catches, which might influence even more the real values of landings. It is urgent the development of comprehensive research programs that promote population studies on this resource and the sustainability of its fishery. For instance, this can be reached by integrating international efforts for exploring the ocean’s diversity in deep regions and promoting the study and assessment of potential new marine resources. The permanent exploitation of this long-lived and slow-growing marine species without further research and strict fishing control could jeopardize, in the medium and long term, not only its fishery but the availability of this marine resource in Peruvian waters.