Rhinitis is one of the most prevalent diseases in the world. Indoor microbiome is confirmed to associate with respiratory diseases such as asthma and infections, but no study reported the association between indoor microbiome and the occurrence of rhinitis. In this study, 370 students were randomly selected from 8 junior schools in Terengganu, Malaysia, and self-administered questionnaire and skin prick tests were conducted to define the allergic and non-allergic rhinitis among students. Vacuum dust was collected from the floor and chair/desk surfaces in the classrooms, and culture-independent high-resolution amplicon sequencing and quantitative PCR were conducted to characterize the absolute concentration of bacterial and fungal species. Hierarchical logistic regression was applied in the association analyses. We found similar microbial associations for the students with allergic and non-allergic rhinitis. The microbial richness in Gammaproteobacteria was protectively associated with allergic and non-allergic rhinitis (p = 0.02 and 0.04), and total fungal richness was positively associated with allergic and non-allergic rhinitis (p = 0.01 and 0.03). The absolute concentration of two bacterial species, Aeromonas enteropelogenes and Brasilonema bromeliae, were associated with both types of rhinitis, and six bacterial and one fungal species was associated with either allergic and non-allergic rhinitis (p < 0.005). Four species previously reported as facultative pathogens, including A. enteropelogenes, Escherichia fergusonii, Enterobacter xiangfangensis and Streptococcus salivarius, were protectively (negatively) associated with rhinitis. A higher concentration of two radiation-resistant species, including Deinococcus gobiensis and Deinococcus grandis, were associated with an increased odds of rhinitis.