Topmouth gudgeon (Pseudorasbora parva), a small freshwater cyprinid species originating from East Asia and spreading to Eurasia and Africa, is an ideal model for studies on invasion ecology and toxicology. However, the genomic or gene resources are still blank in this species, limiting the molecular and genetic analysis. In this study, PacBio Iso-Seq and Illumina RNA-seq were performed on multiple tissues of P. parva to generate large-scale full-length transcripts.