The human microbiome is a collection of microbial species and their associated genomes that live on and in the body. Recent advances in molecular biology methods have revolutionized microbiome analysis techniques. Studies of the airway microbiome have illustrated that the paranasal sinuses are not sterile in the healthy state. Because human airways are in constant contact with the external environment and their mucosal surfaces are colonized with microorganisms, it is assumed that the local microbiota might influence immune homeostasis as well. Chronic rhinosinusitis and allergic rhinitis are the most common chronic airway diseases that yield a significant amount of socioeconomic burden. Despite the problematic nature of the diseases, a thorough understanding of their cause and pathogenesis is still lacking. At present, bacteria are believed to play a pathogenetic role in the propagation of inflammation and it is necessary to establish the relationship between the microbiome and inflammatory patterns to find their clinical reflections and also their possible causal relationship. Such investigations may elucidate the path to therapeutic approaches in correcting an imbalanced microbiome. In this review, we summarized recent typical studies dealing with the upper airway microbiome and discuss their clinical significance focusing on chronic rhinosinusitis and allergic rhinitis.