Abstract: This study was conducted to evaluate the applications of biological filter medias in low C/N ratio aquaculture wastewater. Elastic filler and fluidized bed packing materials were used as biofilm of nitration and PHBV (poly-3-hydroxybutyrate-co-3-hydroxyvalerate) were used as the carbon source and biofilm carrier of denitrification in this study. The water quality and the bacterial community compositions were determined by the method of Miseq high-throughput sequencing. The obtained results demonstrated that biofilm of the system formed after 4 weeks operation, at the temperature of 25—30℃. Our results also showed that the two kinds of media had great effects on removing total nitrogen (TN), ammonia nitrogen (NH₃-N), nitrite (NO₂-N). The removal rate of TN, NH₃-N and NO₂-N can reach up 90%. The sequencing results indicated that the predominant bacteria on the biofilm sample a coating onto elastic filler and fluidized bed packing materials were Proteobacteria, Bacteroidetes and Firmicutes. While the major microorganisms on the biofilm sample b attaching to the surface of PHBV granules were Proteobacteria, Firmicutes, Bacteroidetes, Spirochaetae and Chlorobi. The analysis revealed that both diversity index and abundance index of microbial community of biofilm sample b were far higher than the sample. Family of Comamonadaceae and Rhodocyclaceae belonging to Betaproteobacteria were highly enriched in both biofilms samples. However, there was a distinctive difference in phylotypes between the two biofilm samples at genus level, which was probably due to the diversities of biofilm carrier, carbon source and dissolved oxygen. The genera of biofilm sample a was only two thirds of b. A total of 8 and 18 genera with a relative abundance greater than 0.5% were identified from a and b, respectively. Among them, the unknown groups belonging to Comamonadaceae and Rhodocyclaceae accounted for 56.67% and 45.51% of the total sequence of a and b. Organisms from the genus Magnetospirillum and Nitrospira were only detected in a, while the genus Clostridium, Zoogloea, Cloacibacterium, Desulfovibro etc were identified in b, which probably contributed to denitrification performance.