Triploidization is routinely applied in aquaculture of many commercially relevant fish species. The comparative transcriptomic analysis of ovaries of triploid (3N) and diploid (2N) female rainbow trout revealed a total of 9075 differentially expressed genes. The enrichment of process involved in carbohydrate and lipid metabolism in 2N ovaries can reveal high metabolism of ovarian tissue and the production of energy reservoir essential for the early stages of development. Our results highlight the importance of oocyte hydration as well as estrogen, insulin, leptin, FGF, Notch signaling and pathways related to regulation of cAMP level in oocytes in proper oocyte meiotic maturation prior to ovulation in 2N ovary. Conversely, triploidization may lead to increase in ovarian cellular senescence and apoptosis, which in turn can resulted in abnormal gonadal morphology and fibrosis. The down-regulation in 3N ovaries of genes responsible for the precise regulation of meiosis and the proper chromosome segregation during meiosis probably affects the meiotic maturation by irregular meiotic division of chromosomes. The induction of triploidy of rainbow trout genome resulted in enhance expression of male-specific genes, genes responsible for re-establish the transcriptional balance after genome reorganization and genes involved in regulatory mechanism, including gene silencing and DNA methylation.