In order to investigate the low temperature start-up characteristics of biological aerated filter (BAF) for simulated marine seawater aquaculture wastewater treatment,two zeolite media BAFs,which inoculated with marine sediment and activated sludge respectively,were operated under the conditions of hydraulic retention time 1h,water temperature 12~16℃,the ratio of gas to water 2:1(dissolved oxygen in 3~5mg/L),as well as the influent pH value of 7.38~8.23,permanganate index of 5.11~9.46mg/L,ammonia nitrogen 3.27~4.88mg/L.The results showed that the start-up time,average concentration of effluent ammonia nitrogen,removal rate of average ammonia nitrogen,average concentration of effluent permanganate index and removal rate of permanganate index of BAF inoculated with marine sediment were 39d,0.36mg/L,91%,4.96mg/L,31.9%,respectively,while the BAF inoculated with activated sludge were 35d,0.17mg/L,95.7%,4.63mg/L,36.5%,respectively.It was observed by DGGE and 16SrDNA gene sequencing analysis that the microbial population structure of two reactors had gone through a tremendous change.The Shannon index of original activated sludge,the marine sediment and the corresponding backwashing sludge the reactor stable operation after one month was 2.41,2.63,2.88 and 2.65,respectively.With the increase of running time,the deference of quantity and abundance microbial population in two BAFs decreased gradually,and the dominant population became more and more similar and consistent.Several salt-tolerant ammonia-oxidizing bacteria became dominant species,and the mainly population in stable operated BAF belonged to γ-proteobacteria class.