It has become widely accepted that the spatial complexity of the populations that sustain benthic fisheries necessitates monitoring, assessment, and management procedures. To date, the stocks and fisheries of benthic species in southern Chile have been evaluated and managed following single-species stock approaches, allocating total allowable quotas across internal political boundaries. In the present study, we analyzed fisheries data from 1996 to 2005 and applied two different methodologies to identify harvesting zones aimed at providing a better understanding of the spatial heterogeneity of the multispecies fisheries in southern Chile. As a first method, harvesting zones were defined by experts, followed by a posteriori multivariate analysis. As a second approach, zones were grouped utilizing hierarchical cluster analyses. The results from both classification methods revealed the existence of spatial heterogeneity in the fishery, which did not match current administrative boundaries. The harvesting zones proposed here by the expert panel appear more reliable than those emerging from hierarchical classification methods, and we suggest that these be used as a starting point to guide the spatially-explicit analysis, monitoring, and management of the dominant benthic fisheries. Regardless of the method of harvesting zone identification, our results indicate that the subzoning proposed herein for southern Chile benthic fisheries form a reasonable operative framework for a spatially-explicit adaptive management process. Both zone identification methods provided an insight into understanding the spatial complexity of the fishery and would potentially be useful in the analysis of other benthic coastal fisheries.