Many scholars have explored the treatment effect of biofilters with different packing media. However, there is little report on the microbial communities of the packing media. Therefore, this paper attempts to disclose the differences between two popular packing media of biofilter, namely, volcanic rock and ceramiste, in terms of the attached bacteria. Firstly, two multi-layer biofilters (MBFs) were designed, and respectively packed with volcanic rock and ceramiste. The packing media were collected after the MBFs entered stable operation. The DNA was extracted from the media and pyro-sequenced. After that, the community structure and diversity of the microorganisms were analyzed in details. The main results are as follows: The values of ACE estimator, Chaol estimator, and Simpson's diversity show that volcanic rock had the higher bacterial diversity. The libraries with volcanic rock and ceramsite respectively consist of 1,810 and 1,352 operational taxonomic units (OTUs). Surprisingly, the Venn diagram of OTUs indicates that the two-packing media only share 13.2 % OTUs. The volcanic rock contained sequences in 16 phyla while ceramiste only covered sequences in 11 phyla. Among all phyla, Tenericutes was unique to ceramiste, while Chloroflexi, GN02, NKB19, Thermi, Chlorobi and TM7 were only observed in volcanic rock. Ceramiste contained more Proteobacteria (67.06 % vs. 64.12 %), Bacteroidetes (25.11 % vs. 22.72 %) and Firmicutes (6.20 % vs. 4.55 %) than volcanic rock. The research findings clarify the research direction and provide the theoretical basis for improving ceramiste technology and developing alternatives for volcanic rock.