The present study determined the distribution and biomass of the Peruvian anchovy and pelagic red squat lobster related to the oceanographic characteristics in the marine protected area of the Paracas National Reserve in the Northern Humboldt Current System. Acoustic, biological, and oceanographic information was collected on the pelagic habitat in surveys carried out by the Peruvian Marine Research Institute during the summer and spring of 2018, 2019, and 2020. The results obtained indicated that the spatial occupation of the pelagic habitat of Peruvian anchovy and pelagic red squat lobster were influenced by the dynamics of upwelling, water masses, and a shallow and intense Oxygen Minimum Zone. Spatial overlap of high biomass of Peruvian anchovy and pelagic red squat lobster were recorded in the surface layer during the night. Although, with the presence of dense swarms of múnida in anoxic intermediate waters of the Oxygen Minimum Zone during the day. The Marine Protected Area off the Paracas National Reserve functions as a protection zone for the structure and functioning of the pelagic-neritic ecosystem and strengthens the fishery production of Peruvian anchovy stock in the Northern Humboldt Current System.