Fish possess a remarkable multitude of sex determination/differentiation systems to facilitate their adaptation to dynamic changes in the environment. Recent evidence has indicated that the sex-determination/differentiation system in fish is sensitive to a number of extrinsic/environmental factors such as population density, social behaviors, pH and dissolved oxygen levels. Hypoxia is one of the most widespread and pressing environmental problems in aquatic environments worldwide, causing severe habitat loss and interruption of ecosystem balance. Recent studies by our group have shown that hypoxia is an endocrine disruptor that impairs sex differentiation and reproductive functions in fish, leading to male-biased F1 populations of zebrafish and Japanese medaka. Such shifts in sex ratio are likely to have dire consequences for reproduction and recruitment of fish assemblages inhabiting small waterbodies, potentially leading to losses in biodiversity and fishery productivity. Despite this emerging threat, the molecular mechanisms through which hypoxia alters fish sex differentiation, and hence sex ratios, remains poorly understood. As an initial step to investigate the potential role of miRNAs in mediating hypoxia-induced male-biased sex ratios in fish, we recently conducted small RNA sequencing on marine medaka (Oryzias melastigma) embryos that were exposed to hypoxia for 6 days (during a critical time window of sex determination). In addition, we successfully established brain and gonadal miRNA transcriptomic libraries from male and female adult medaka fish for comparison and identified a number of tissue- and gonad-specific miRNAs in adult marine medaka as well as specific hypoxia-responsive miRNAs from medaka embryos. Bioinformatic analyses predicted that some of the hypoxia-responsive miRNAs specifically target the 3′-UTR of the androgen receptor (AR) gene. It is widely known that AR is a steroid hormone receptor that plays a critical role in male gonad differentiation and development, and in the maintenance of secondary male characteristics in vertebrates. Using the marine medaka as a fish model, we propose to test the hypothesis that the activation/inhibition of specific hypoxia-responsive miRNAs, directly or indirectly targeting AR expression or AR-associated factors, represent an important regulatory hub controlling sexual differentiation and development in fish and may provide a molecular basis for hypoxia-induced male-biased sex ratios in fish.