Bivalve microbiota play a vital role in host health, supporting nutrient processing, immunity, and disease resistance. However, the increasing hypoxia in Chilean coastal waters, caused by climate change and eutrophication, threatens to disrupt this microbial balance, potentially promoting pathogens and impairing essential functions. Mytilus chilensis is vulnerable to hypoxia-reoxygenation cycles, yet the effects on its microbiota remain poorly understood. This study investigates the impact of hypoxia on the structure and functional potential of the microbial communities residing in the gills and digestive glands of M. chilensis. Employing full-length 16S rRNA gene sequencing, we explored hypoxia's effects on microbial diversity and functional capacity. Our results revealed significant alterations in the microbial composition, with a shift towards facultative anaerobes thriving in low oxygen environments. Notably, there was a decrease in dominant bacterial taxa such as Rhodobacterales, while opportunistic pathogens such as Vibrio and Aeromonas exhibited increased abundance. Functional analysis indicated a decline in critical microbial functions associated with nutrient metabolism and immune support, potentially jeopardizing the health and survival of the host. This study sheds light on the intricate interactions between host-associated microbiota and environmental stressors, underlining the importance of managing the microbiota in the face of climate change and aquaculture practices.