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The heterogeneity of the lung microbiome and its alteration are prevalently seen among chronic lung diseases patients. However, studies to date have primarily focused on the bacterial microbiome in the lung rather than fungal composition, which might play an essential role in the mechanisms of several chronic lung diseases. It is now well established that <i>Aspergillus</i> spp. colonies may induce various unfavorable inflammatory responses. Furthermore, bacterial microbiomes such as <i>Pseudomonas aeruginosa</i> provide several mechanisms that inhibit or stimulate <i>Aspergillus</i> spp. life cycles. In this review, we highlighted fungal and bacterial microbiome interactions in the respiratory tract, with a focus on <i>Aspergillus</i> spp.