This study compares the prevalence and abundance of the isopod Edotia doellojuradoi in the mussel Mytilus edulis, between water column rope farming systems and nearby natural benthic beds at Puerto Raúl Marín Balmaceda (43° 46' S, 72° 57' W), Aysén, Chile, taking into account the maximum shell length of the host as a covariate. In addition, the damage caused by E. doellojuradoi was assessed with the visual inspection of the gills, according to the protocol of Zaixso et al. (2009). The isopod was found almost exclusively in natural benthic habitats, where the prevalence increased with the length of the host. The isopod is a macroparasite and not a commensal as previously suggested because it causes gill damage to the mussel, which increased with the abundance of E. doellojuradoi. In addition, maximum body length of female isopods (but not males) increased with the maximum shell length of M. edulis. These results indicate that farming systems are an artificial ecological refuge for the host against this parasitism. The absence of isopods from farming systems may be in part explained by the poor swimming abilities of dispersing isopods. Reports in natural benthic beds from the Atlantic Ocean indicate that the prevalence of E. doellojuradoi is much higher than in the Pacific Ocean, where they attain maximum values in mussels intermediate in shell length, which are similar to our smallest specimens. These results, besides of implying an enlargement of the geographical distribution of the isopod in the Pacific Ocean, justify the need for more studies on the scales of spatial variation of this harmful parasitism in natural benthic beds.