<p>The Japanese eel (<i>Anguilla japonica</i>) is a catadromous migratory fish with a high economic value. The gonads of captive eels do not mature naturally. Under artificial maturation, the hypothalamic-pituitary-gonadal (HPG) axis is activated, and the maturation coefficient of the gonads increased significantly. Prior research investigations into Japanese eel breeding have primarily focused on elucidating the mechanisms underlying gonadal development. However, the problems plaguing the artificial breeding of Japanese eels have remained unsolved. Additionally, the insights into the molecular mechanisms within the pituitary, which acts as an upstream regulatory hub, and its impact on ovarian development are limited. To address these, the pre-matured pituitary (PP) and artificially matured pituitary (AP) tissues from female Japanese eels were subjected to transcriptomics using a method combining PacBio Iso-seq with Illumina RNA-Seq. PacBio sequencing produced 19576 filtered consensus sequences from PP and 39828 from AP. Then, we predicted gene regulatory elements such as alternative polyadenylation, transcription factors, and long noncoding RNAs. A total of 3016 differentially expressed genes (DEGs) were identified based on the Illumina RNA-seq data. Further gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed. Several DEGs that were upregulated in the pituitary were identified. These genes, including <i>nr5a2, pgr, greb1, smad4, bmp5, ar, lhb, adcy5</i>, and <i>tgfbr3</i>, most likely regulate downstream gonadal development <i>via</i> the pituitary. In conclusion, this study obtained the differential expression and full-length transcriptomes of the pituitary in the pre-matured and artificially matured female Japanese eel. These results offer substantial evidence for developing more efficient sex hormones during the captive breeding of eels, while also furnishing a scientific basis for the conservation of eel resources.</p>