Abstract: Three benthic biotic indices, AZTI marine biotic index (AMBI), benthic opportunistic polychaetes amphipods (BOPA), and benthic polychaetes amphipods (BPA), combined with Shannon diversity index (H) were applied in ecological quality status (EQS) assessment, to investigate their suitability at four bays and an estuary in Fujian Province. The results showed that there were substantial differences in the performance of these indices. There were only four sites with the same assessment grades using different indices, accounting for 8.7% of the applied sites. AMBI classified 76.1% of the sites as “Good”, while 89.1% of the sites were classified as “High” using BOPA. The assessment results of BPA and H showed obvious gradient changes. For the bay areas, all the BOPA, BPA and AMBI values had no significant correlation with dissolved inorganic phosphate (DIP) and dissolved inorganic nitrogen (DIN) concentrations, suggesting that these indices did not respond to eutrophication pressure. The H value was significantly and negatively correlated with DIN concentration. For the estuarine area, the three indices, i.e . BOPA, BPA and AMBI, had significantly positive correlations with DIN and DIP, and there was no clear spatial variation in the assessment grades of these indices with the distance toward sea. The results suggested that BOPA, BPA and AMBI would overestimate the EQS and would show no response to the eutrophication pressure in estuarine area. Similar to the result from the bay areas,H value in the estuary area was significantly and negatively correlated to DIN. Meanwhile, the assessment grades of the seven sections in the estuary tended to increase with the distance toward the sea. In summary, our results suggested that BOPA, BPA and AMBI would not be suitable for the EQS assessment for Fujian coastal area, while H would be more suitable as it could respond to the main anthropogenic pressures.