The origin and contribution of seminal plasma RNAs into the whole semen RNA repertoire are poorly known, frequently being overlooked or neglected. In this study, we used high-throughput sequencing and RT-qPCR to profile microRNA (miRNA) constituents in the whole semen, as well as in fractionated spermatozoa and seminal plasma of Atlantic salmon (Salmo salar). We found 85 differentially accumulated miRNAs between spermatozoa and the seminal plasma. We identified a number of seminal plasma-enriched and spermatozoa-enriched miRNAs. We localized the expression of some miRNAs in juvenile and mature testes. Two abundant miRNAs, miR-92a-3p and miR-202-5p, localized to both spermatogonia and somatic supporting cells in immature testis, and they were also highly abundant in somatic cells in mature testis. miR-15c-5p, miR-30d-5p, miR-93a-5p, and miR-730-5p were detected only in mature testis. miRs 92a-3p, 202-5p, 15c-5p, and 30d-5p were also detected in a juvenile ovary. The RT-qPCR experiment demonstrated lack of correlation in miRNA transcript levels in seminal plasma versus blood plasma. Our results indicate that salmon semen is rich in miRNAs, which are present in both spermatozoa and seminal plasma. Testicular-supporting somatic cells are likely the source of seminal plasma enrichment, whereas blood plasma is unlikely to contribute to the seminal plasma miRNA repertoire.Teleost fishes are the largest group of vertebrates, and their predominant reproductive features, such as a lack of accessory glands in semen production, external fertilization, or spermatozoa activation upon contact with water [10], make them distinct from tetrapods. Virtually, nothing is known about the potential transfer and possible role of paternal RNAs in embryo formation in fish.The whole semen RNAs are found not only in germ cells (spermatozoa) but also in the seminal plasma, where they are bound in protein complexes and encapsulated in microvesicles [11,12]. Seminal plasma is an important constituent of semen and has a vital role in spermatozoa metabolism, survival, and motility. It contains inorganic and organic compounds, proteins, and RNAs [13]. In fish, seminal plasma has been implicated in osmotic balance, proteolytic activities, and fertilization success [14-16]. However, the repertoire, abundance, origin, and functions of seminal plasma RNAs remain unknown in fish.Micro RNAs (miRNAs) are among the RNAs that are present in the sperm of vertebrates. These non-coding RNAs, approximately 22 nucleotides long, function mainly in translational suppression by binding at 3 UTR of mRNA to regulate various biological processes, including spermatogenesis [17]. In mouse, ingression of sperm miRNA to oocytes causes heritable epigenetic change in gene expression [18]. In addition, a sperm-borne miRNA miR-34c is essential for the first cell division [2]. miRNA expression has been characterized in the testes of some teleost fish [19], such as Atlantic halibut Hippoglossus hippoglossus [20], Atlantic cod Gadus morhua [21], yellow catfish Pelteobagrus ful...