Based on biologic and environmental materials collected from coastal areas of Bohai Bay (China) in April, 2008, three biotic indices (AZTI’s Marine Biotic Index (AMBI), Shannon–Wiener Index and -statistic) were applied together to evaluate the ecological status of the sampling area. The results showed a clear spatial gradient from a worse ecological status in the near-shore areas (especially around Haihe and Jiyun River Estuaries) to a better status in the offshore areas. While all the three indices could assist decision makers in visualizing spatial changes of organic pollutants in Bohai Bay, two indices, i.e., AMBI and Shannon-Wiener index, were effective in distinguishing sites from Haihe River Estuary, Jiyun River Estuary and other area. However, -statistic can’t tell the differences between estuaries and other area. It would be explained that organic pollutants and/or other environmental stresses in Bohai Bay were not strong enough to reduce the size of macrozoobenthos, which may cause both of the abundance and biomass curves crossed. To our knowledge, this is the first time that several benthic indices were used to assess the benthic ecological status in Bohai Bay, which gave the similar results. Furthermore, there is indication that the ecological status is related to excess input of wastewater along main rivers and outlets. In a word, AMBI, Shannon–Wiener Index and -statistic could be able to assess the benthic ecological status of Bohai Bay under the organic pollutants pressure.