Mollusks comprise one of the largest phylum of marine invertebrates. With their great diversity of species, various degrees of mobility, and specific behavioral strategies, they haveoccupied marine, freshwater, and terrestrial habitats and play key roles in many ecosystems. This success is explained by their exceptional ability to tolerate a wide range of environmental stresses, such as hypoxia. Most marine bivalvemollusksare exposed to frequent short-term variations in oxygen levels in their marine or estuarine habitats. This stressfactor has caused them to develop a wide variety of adaptive strategies during their evolution, enabling to mobilize rapidly a set of behavioral, physiological, biochemical, and molecular defenses that re-establishing oxygen homeostasis. The neuroendocrine system and its related signaling systems play crucial roles in the regulation of various physiological and behavioral processes in mollusks and, hence, can affect hypoxiatolerance. Little effort has been made to identify the neurotransmitters and genes involved in oxygen homeostasis regulation, and the molecular basis of the differences in the regulatory mechanisms of hypoxia resistance in hypoxia-tolerant and hypoxia-sensitive bivalve species. Here, we summarize current knowledge about the involvement of the neuroendocrine system in the hypoxia stress response, and the possible contributions of various signaling molecules to this process. We thusprovide a basis for understanding the molecular mechanisms underlying hypoxic stress in bivalves, also making comparisons with data from related studies on other species.