<p>Red tilapia has gained increasing popularity worldwide in the commercial aquaculture production due to its rapid growth and delightful taste. However, the occurrence of skin colour variation poses a significant challenge to the advancement of commercial culture. Furthermore, the molecular regulatory mechanism and genetic basis for the distinct skin colouration in red tilapia remain undisclosed. In this study, a comprehensive transcriptome analysis was conducted on red tilapia with different skin colour by integrating PacBio Iso-seq technology with Illumina short-read sequencing methods. A total of 41.38 Gb of clean data was generated, resulting in the acquisition of 30,970 transcripts. Among them, 10,829 transcripts were successfully annotated in at least one public database. In addition, 10,827 coding sequences, 452 transcription factors, and 781 lncRNAs were identified in new transcripts. Furthermore, we performed RNA-seq analysis to identify skin colour-associated genes in red tilapia with three colour spots (white spots, W; black spots, B; red spots, R). The results revealed the identification of 278 differentially expressed genes (DEGs) between the comparison groups, which included B vs R, B vs W, and W vs R. Among them, some known genes were found to be involved in regulating the skin pigment synthesis, including PMEL, Wnt-4, melanoregulin and ALK in red tilapia with different skin colour. In addition, some pathways, including melanogenesis (ko04916), ECM-receptor interaction (ko04512), Hedgehog signaling pathway (ko04340) and steroid hormone biosynthesis (ko00140), were associated with the skin pigment synthesis in red tilapia. Furthermore, the quantitative real-time PCR analysis confirmed a moderate correlation (coefficient of 0.68) between the results obtained from the qPCR and RNA-seq methodologies. In summary, our findings will significantly contribute to the enhanced comprehension of the molecular regulatory mechanisms underlying the variation in skin colour observed in red tilapia.</p>