BACKGROUND: Natural M. chilensis populations dominate habitats with a steep environmental gradient, and that are characterized by abrupt changes in salinity and exposure to desiccation. Although these populations are the source of seed supplies for the Chilean mussel culture industry (annual production around 250 thousand Tons), knowledge about natural populations is scarce. Based on video transect recordings, this study carries out research into one of the principal mussel beds and its associated epibenthic community in the Reloncaví Fjord, both along cross-shore and along-shore distribution gradients RESULTS: Mytiluschilensis was observed between the middle intertidal zone and the upper subtidal zone (between approximately 9 and 26 psu), with a richer associated community towards the subtidal zone and the fjord mouth. The mussel Condition Index (total meat weight/shell length*100) in the intertidal zone was significantly greater than in the subtidal zone, which raises questions about the reproductive contribution of mussels along the intertidal mid-subtidal gradient CONCLUSIONS: Salinity and tidal variations, together with biological interactions, would seem to be key factors for explaining M. chilensis spatial distribution in the Reloncaví fjord, where beds appear to be in a contraction stage, as evidenced by M. chilensis scarcity towards the subtidal zone. The importance of these populations and their persistence in environments with high perturbation frequency, suggests a monitoring program should be implemented that considers both population spatial distribution and the changing environmental conditions.