[Aim]  Analyzing differences in symbiotic flora between healthy and sub healthy states of Dermatophagoides farinae and their effects on the host. [Methods]  Full-length sequencing of the 16S rRNA gene of laboratory-reared dust mites in the healthy (FM) and sub healthy (MF) groups was performed using Pacbio triple sequencing, and the characteristics of the comparative colonies were characterized by OTU clustering, Alpha/Beta diversity, and KEGG functional prediction. [Results]  A total of 169 740 valid sequences of bacterial 16s rRNA in dust mites were obtained, clustered into 72 OTUs, and annotated to 13 phyla, 21 orders, 31 orders, 47 families and 62 genera of bacterial taxa. Compared to the healthy group, the sub-healthy group exhibited higher alpha diversity (Shannon index = 1.47), and specific bacterial genera, such as Lysinibacillus, contributed significantly to the observed differences, indicating distinct symbiotic bacterial structures in dust mites under different health conditions. Beta diversity analysis showed differences in the composition of commensal bacteria between the healthy and sub-healthy groups, but without statistical significance (P > 0.05). Functional analysis showed that both groups had a higher abundance in substance metabolic pathways. [Conclusion]  Different health states of dust mites are accompanied by changes in the structure of symbiotic flora, and specific bacterial genera with pathogenic potential (e.g., Lysinibacillus) may be involved in host pathology, providing theoretical support for the development of targeted acaricides.