Polychaetes are a key group in marine benthic communities worldwide because they are ubiquitous and generally abundant and diversified at all depths. Their anatomical complexity, however, makes it very difficult and time consuming to identify them correctly to species level, increasing the costs of any study involving them. Thus, the use of higher taxonomic levels in this group is a useful tool in monitoring or pollution-related studies. In this study, we compared the results obtained at both the species and family levels to assess the faunal changes associated to the different environmental conditions in the southern Gulf of Mexico, a large region known for its ecological and economic importance. We collected and identified 5686 polychaetes from 44 families, 95 genera and 206 species at 68 stations. Their relative density varied from 0% to 29.3% (ind. l−1) being higher in the Campeche Bank. The family richness (1–17) and specific richness (1–46) were both higher in the Campeche Bank. The same pattern was found for diversity and evenness at both taxonomic levels analyzed. The absolute diversity values were different using different taxonomic levels, but increased or decreased similarly at both levels. With the non-metric multidimensional scaling analysis, two main groups of stations emerged: Campeche Bank and Campeche Sound, with two less defined groups indicating a transitional sedimentary zone between them. All the groups were consistent both at family and species level, indicating little loss of information when the family level is used instead of the species level. We conclude that, if good previous basic knowledge of that fauna exists, the family level can be used to monitor environmental and pollution effects in these types of bottoms.