Abstract: According to the macrobenthos monitoring results during 2004~2013 in Lingshui Xincungang and Li'angang Seagrass Special Protected Area,Hainan,a total of 95 macrobenthos species were found.Mollusks were the most dominant groups in the term of species numbers.During the years 2009~2013,the average abundance was 137.53 ind/m2,and the average biomass was 167.57 g/m2.Two community groups were divided according to CLUSTER and MDS analysis based on macrobenthos abundance data,which were highly related with the organic carbon content in sediment (P0.01).The important environmental factors controlling the macrobenthos community structure were organic carbon content,Mdф,QDф,and seagrass coverage.The biodiversity indices indicated that there was obvious difference among monitoring years.The ABC curves showed that the monitoring years were under disturbance at different levels except XC2011 under no disturbance.Compared with the data in 2002,the average abundance and biomass of macrobenthos have decreased greatly.The above results indicated that the special protected area was under higher effect of anthropogenic activities and the pollution of different degrees,which causes the changes of macrobenthos community structure.