Advances in the optimization of abalone culture can be achieved through a deeper understanding of the molecules modulating physiological functions including growth, metabolism, and reproduction. To identify neuropeptide molecules that play key roles in the modulation, transcriptome analysis of the ganglia (e.g., cerebral and pleuropedal ganglia) of the abalone Haliotis discus hannai was performed. The long-read single-molecule real-time sequencing using the PacBio RSII platform generated 48,344 full-length transcripts, with an N50 length of 3,020 nucleotides (nt), a GC ratio of 44.76%, and a size range of 309–17,545 nt. Of these transcripts, 32,901 (68.1%), 40,515 (83.8%), 7,591 (15.7%), and 14,945 (30.9%) were annotated using the NCBI nonredundant, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Cluster of Orthologous Groups databases, respectively. Using in silico data mining, 18 putative neuropeptide genes were identified from the transcriptome of H. discus hannai. Comparative analysis revealed that the sequences of identified neuropeptides of H. discus hannai were conserved with other molluscan neuropeptide homologs; however, some features of H. discus hannai neuropeptides were found distinct from those of other molluscan neuropeptides. Interestingly, this is the first study to report a precursor encoding a DYamide peptide in molluscan, which is likely to be a homolog of DLamide peptides, which have been discovered only in annelids to date. This study provides comprehensive neuronal transcriptome data for H. discus hannai, which could help improve aquaculture methods both practically and economically by providing a basis for neuroendocrine-based strategies.