Biological traits analysis (BTA) is considered to be a powerful technique for describing the ecological functioning of marine benthic assemblages. This study is the first to apply BTA to assess differences in the traits of benthic faunal assemblages between areas exposed to heavy and light trawling in a major upwelling ecosystem along the west coast of southern Africa. The data were collected from two sampling locations in Namibia and six sampling locations in South Africa. The intensity of trawling varied from area to area. Significant differences in biological traits (BT) were detected between heavily and lightly trawled areas. Weighted infaunal traits showed significant differences between heavily and lightly trawled areas for 17% of the traits investigated, while 24% of epifaunal traits investigated were significantly different between areas of different trawling intensities. This suggests that the measured BTs of the epifauna might be more sensitive to trawling disturbances than BTs of the infauna. The infaunal traits differed significantly between areas with larger or smaller proportions of sand and mud. Nevertheless, more of the significant differences in infaunal BTs were related to variations in trawling intensity than to variations in sediment composition. Significant modifications of BTs are likely to lead to modified functioning of the community and provide more general potential indicators for management than those based on species. The study confirms the need for more basic biological and life history data on macro-benthic invertebrates but nevertheless shows that BTA detected specific features that correlate with trawling intensity and that these features may be important for epifaunal assemblage functioning.