The red squat lobster Pleuroncodes monodon is an important fishery resource in the Humboldt Current System (HCS). This decapod is exploited in two fishing units: (a) the northern fishing unit (NFU, from 26°S to 30°S) and (b) the southern fishing unit (SFU, from 32°S to 37°S), each of which have an adjacent nursery area that is the source of recruits to replace the exploited adult populations (in the NFU: off the coast of Coquimbo (28°S) and in the SFU: off the coast of Concepción (36°S)). Marked spatial differences in the environmental conditions of the NFU and SFU, and the biogeographic break that exists between these nursery areas (30°S) may promote changes in the bioenergetic condition of new P. monodon juveniles. To evaluate this, we analyzed the bioenergetic condition (measured as: body mass, lipids, proteins, glucose, and energy) of new juvenile females in the main nursery areas off the Chilean coast. The juvenile females from the SFU showed a higher body mass than those from the NFU. Consistently, the juvenile females from the SFU had a higher content of lipids, proteins, and glucose than those from the NFU, indicative of higher energy contents and a higher lipid/protein ratio in the south compared to the north. Considering the current overexploitation of this fishery resource in the HCS, it is essential to understand how the bioenergetic condition of juvenile females of P. monodon may vary in nursery areas at different latitudes in order to generate sustainable fishery management policies with an ecological approach, designed specifically to each fishing unit. Furthermore, identifying the latitudinal variations of these biochemical compounds in P. monodon juveniles can elucidate the geographic origin of red squat lobsters that present a ”better bioenergetic condition” in the HCS, which may significantly benefit sustainable fishing certification processes.