Located approximately 360 nm off the coast of Chile there is a disjoint realm of two small oceanic islands systems, the Juan Fernandez and the Desventuradas archipelago. Currently the local economy of the islands is almost exclusively supported by the harvest and trade of marine resources, focusing mainly on the exploitation of the rock lobster (Jasus frontalis). This endemic species is distributed in both archipelagos, forming a metapopulation, whose population structure and dynamic is modulated by oceanographic forcing, especially during its extended planktonic larval phase. The population structure and the conection-retention within and between islands was assessed, based on the use of coupled biophysical model (the hidrodynamics model OFES and an individual-based model of J. frontalis). The analysis of the hydrodynamic model predictions showed the presence of mesoscale structures associated with the islands systems. The simulation results indicated significant levels of connectivity-retention within and between island systems showing also a strong interannual variation of these. Biophysical modeling results indicated that recruitment varibility associated with the Juan Fernandez archipelago depends mainly on larvae originated within this system, which as well will contribute with recruits to the Desventuradas archipelago. The sensitivity analysis of the biophysical model to identify the potential biophysical forcing of the dependent variables of the model (e.g. connectivity-retention index), resulted in that temporal and spatial patterns reproductive larval stage duration and season (year) are highly significant factors. Finally, a metapopulation structure for J. frontalis, with a high level of connectivity in the archipelago of Juan Fernandez and a considerable amount of larvae in the Desventuradas islands is proposed. These fluxes are determined mainly by the coupling between prevailing biological and oceanographic factors.