In order to study the diversity of eukarytic nanoplankton in the sea area for scallop culture,and clarify the relationship between eukaryotic nanoplankton and transmission of zhikong scallop (Chlamys farreri) acute viral necrosis virus(AVNV),seawater samples were collected monthly in 2009 and 2010 from Qingdao Liuqing River Bay’s sea area.3-25 μm plankton components were filtered and amplified 18S rDNA variable region sequences from filtered samples were analyzed by DGGE technique.The results show that the main eukaryotic nanoplankton in the sea area included Dinozoa,Ciliophora,Euglenozoa,Haptophyta,Ochrophyta,Labyrinthulomycota,Cryptista,Choanozoa,Amoebozoa and Cercozoan.The amount of Dinozoa and Ciliophora was the highest at 41% and 38.2%,respectively.The cluster analysis based on mensal DGGE bands shows that the plankton community from May to November 2009 is similar in the diversity of eukarytic nanoplankton.According to the studied results on scallop AVNV,Skeletonema costatum was taken to be a vector of transmission of AVNV,and it distributed during the period of scallop massive death.However,the role of Dinozoa and Ciliophora during the transmission of AVNV has yet to be determined.