Background: Polyploidy is an important force to improve biological evolution. Chromosomal ploidy manipulation is one of the means to create excellent germplasm. It has an important significance to understand the effect of genome duplication on fertility in polyploidy breeding. In this study, coding and non-coding RNAs involved in gonadal development were characterized, and their relationships were explored. Results: By high-throughput sequencing, we compared the expression profiles of gonadal mRNA, long non-coding RNA (lncRNA), and microRNA (miRNA) at different developmental stages [65 days post fertilisation (dpf), 180 dpf, and 600 dpf] between the diploid (XX) and triploid (XXX) rainbow trout. A majority of differentially expressed (DE) RNAs was screened. The overlapped DE mRNAs of three stages were functionally annotated by Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. According to the overlapped miRNAs, the predicted miRNA-mRNA/lncRNA network was constructed based on the target pairs of lncRNA-miRNA and mRNA-miRNA. Also, RT-qPCR was performed to validate the credibility of the network. Conclusions: Lots of lncRNAs involved in fertility were characterised by this network, which provided a reference sequence for further research. In summary, this study explored the potential interplay between coding and noncoding RNAs during the gonadal development of polyploid fish and elaborated the effect of triploidization on fertility.