Abstract: According to the data of environmental survey on harmful substances in seawater, surface sediments and cultured organisms from shellfish-culture areas of Lianjiang southeast sea area in April, June and August 2009, ecological environment quality of shellfish-culture areas was classified by the shellfish culture ecological environment quality synthesis assessment index method. The results showed that no area belonged to the first class, 46 areas with the area of 2978 hm2 (occupied 82.1% of all areas) belonged to the second class, and 10 areas with the area of 280 hm2 (occupied 17.9% of all areas) belonged to the third class in the 56 shellfish-culture areas of Lianjiang. To the second class, there were 14 areas belonged to 2a class, 24 areas belonged to 2b class and 8 areas belonged to 2c class. To the third class, there were 7 areas belonged to 3a class and 3 areas belonged to 3b class. The third class area was located in the Sinonovaculla Constricta beach culture areas of Aojiang estuary and Minjiang estuary, which corresponded with the investigation on the state of eco-environment in shellfish-culture areas of Lianjiang. compared between the synthesis assessment index method and the single parameter assessment method of escherichia coli quality. The results indicated that all the areas belong to the first class besides the mytilus edulis culture area belonging to the second class in the Houcaili Bay. These results have certain disparity with the classification by the synthesis assessment index method.