The Magnuson–Stevens Fishery Conservation and Management Act of 2006 required that regional fishery management councils implement annual catch limits and accountability measures for all federally managed stocks by 2011. Many managed species are data limited and no formal stock assessment has been done for them. One possible approach to managing unassessed species is to assign them to assemblages that are managed as units. The utility of this approach was evaluated using fishery‐dependent and fishery‐independent data from the Gulf of Mexico. Multivariate statistical analyses revealed several consistent assemblages among the 42 reef fish species managed by the Gulf of Mexico Fishery Management Council. Pearson correlation matrices, nodal analyses, and a weighted mean cluster association index integrated results across cluster analyses and provided additional guidance regarding the placement of rare species into groups. Productivity–susceptibility analysis and life history were also considered, as differences in productivity, vulnerability, life history, and other population‐dynamic parameters for the species within complexes might imply different population responses to a similar change in fishing mortality. Identified linkages between species also provide guidance for the impacts of regulations on multispecies fisheries.Received December 31, 2014; accepted February 18, 2015