Benthic community structure and diversity have been investigated to assess stress conditions of Todos os Santos Bay, Bahia, Brazil, as a possible result of the extraction, transportation and refining of petroleum, activities carried out in this area for more than 40 years. Samples were collected over two years, at four stations under the direct influence of stress-causing activities and at a control station. Benthic indices were calculated for all intertidal communities. The density, relative abundance, frequency of occurrence, diversity, similarity and occurrence of preferential species were recorded. Linear correlation indices were calculated to establish comparisons between ecological parameters of the studied communities and concentrations of heavy metals, hydrocarbons, petroleum pollution indicators and sediment mud percentages. The polychaete worms were the dominant group — up to 92% dominance in the community within the influence of refinery activities. Diversity indices indicated significant stress related spatial gradients tied to petroleum. The refinery sample station showed notable differences in its biodiversity figures compared to the other stations. Quantitative benthic indices showed negative correlations between the presence of cadmium, hydrocarbons, n-alkanes and the unresolved complex mixture in the intertidal zone marine sediments.