For example, changes may occur in DNA methylation, covalent modification of histones, or the activation or silencing of genes by miRNAs. MiRNAs have been shown to modulate cellular differentiation and development, and various hypoxia-responsive miRNAs have been reported in human breast and colon cancers. Although the functional roles of several HRMs have been extensively studied in mammals, the biological roles of miRNAs in fish remain poorly understood. Small freshwater fish models have been used extensively to identify and study biological responses to stresses in the freshwater environment. The marine medaka has been developed as a small fish model for similar studies in the marine environment. However, the miRNA profile of this species is unknown. New technologies such as high throughput RNA sequencing have rapidly increased the rate of miRNA discovery. The high sensitivity of RNA-Seq allows for both the detection of species-specific, conserved miRNAs and the detection of weakly expressed miRNAs. MiRNA discovery has often relied on the mapping of small RNA sequence reads to a reference genome. Because a reference genome is currently not available for O. melastigma, predicting miRNAs in this species is difficult. However, with the development of alignment-type methods such as BLAST for identifying homologs of known miRNAs, it has become possible to predict candidate miRNAs in the marine medaka. This is the first report on the identification and expression profiles of miRNAs in male and female O. melastigma, and also the differential responses of selected miRNAs to hypoxic stress. The results presented here will be invaluable for future transgenerational studies and risk assessment using this model marine fish species. The complete genome sequence of the O. melastigma has yet to be reported; thus, the established methods for novel miRNA discovery that involve mapping to the genome are not yet possible. The primary aim of the present study is to identify the known miRNAs in the organs along the brain-pituitary-gonad axis and the center of detoxification, liver in marine medaka. All of these organs are important for ecotoxicological studies. BLAST-based method was utilized to identify 223 distinct miRNA candidates in the brain, ovary, testis and liver of marine medaka based on homology to reported orthologous miRNAs. Using high-throughput sequencing, we identified unique miRNAs with expression levels ranging from 6 to nearly 27,000 RPM. Thus the methodology was BAY-60-7550 highly sensitive and had sufficient dynamic range to detect miRNAs with both high and low expression levels. Our qRT-PCR analysis further confirmed that the identified O. melastigma miRNAs are authentic miRNAs, which are differentially expressed by specific tissue and sex. The miRNAs were also highly tissue specific, with the majority brain-enriched. Many identified O. melastigma miRNAs in the present study are found to be highly conserved between species and taxa.