Abstract: At the end of July 2015, the benthic macrofauna were investigated in sandy intertidal zone in Chinese Horseshoe Crab Reserve in Pingtan island.The results showed that both the larvae and adult of Chinese horseshoe crab were not found in sandy intertidal zone in Shanqi bay and Tannan bay.It was confirmed that Tachypleus tridentatus stayed in an endangered situation in the two bays.The species number, species diversity index (H'), evenness index (J) and abundance index (d) of benthic macrofauna in Shanqi bay were all higher than those in Tannan bay, while the density and biomass of benthic macrofauna in the intertidal zone of Shanqi bay were lower than those in Tannan bay.The difference of benthic macrofaunal community between Shanqi bay and Tannan bay was related to the distribution of Umbonium costatum.The density of Umbonium costatum was high in Tannan bay, but it was few in Shanqi bay.The values of AZTI's Marine Biotic Index (AMBI) and Multivariate Marine Benthic Index (M-AMBI) showed that the ecological and environmental status both in Shanqi bay and Tannan bay were slightly disturbed.The mariculture was the key factor in Shanqi bay, because the suspending aquatic organisms and floats retarded hydrodynamic force led to muddy sediment in lower intertidal zone in Shanqi bay.Tannan bay is a tourism region, where has more artificial tread than Shanqi bay.