Puntius tetrazona is a small tropical ornamental fish with high economic value. Through the method of t-test, the body length (BL), caudal fin length (CL), segment number (SN) and segment length (SL) of caudal fin of P. tetrazona (wild type, WT) and (long fin, LF) were statistically analyzed. The results showed that there was no significant difference in BL between the WT (n=30) and LF (n=30) (P>0.05), but there were significant differences in CL (P<0.000 1), SN (P<0.000 1) and SL (P<0.000 1). At the same time, linear regression analyses were performed on the caudal fin length, segment number and length of caudal fin of WT (n=80) and LF (n=80) P. tetrazona with different body length. The results showed that compared to WT, the caudal fin of LF P. tetrazona grew more rapidly (WT: k=0.28, LF: k=0.62, P<0.000 1), the increasing frequency of the segment number of caudal fin was similar (WT: k=0.79, LF: k=0.82, P=0.006), and the segment length of caudal fin was much greater (WT: k=0.000 4, LF: k=0.006 8, P<0.000 1). Transcriptome analysis of caudal fin of WT and LF adults showed that 56 271 unigenes were obtained from de novo transcriptome assembly. There were 1 304 differentially expressed genes between WT group (n=3) and LF group (n=3), of which 971 genes were up-regulated and 333 genes were down-regulated. The KEGG pathway enrichment analysis showed that the differently expressed genes were significantly enriched into cell cycle and DNA replication signal pathways related to cell proliferation (P<0.05), in which cyclin (cycA, cycB, and cycE) and cyclin-dependent kinase 1 genes were significantly up-regulated. Finally, we determined the expression level of cytoskeleton associated protein 2-like, proliferation marker protein Ki-67, cell division cycle protein 20, protein regulator of cytokinesis 1, up-regulator of cell proliferation and cyclin-dependent kinase 1 by qRT-PCR. The results of qRT-PCR were consistent with those of RNA-seq. The above results showed that a mutated gene in LF P. tetrazona caused the up-regulated expression of cell cycle related genes, which accelerated the cell proliferation rate of caudal fin and resulted in increase of caudal fin segment length, showing the phenotype with a long caudal fin.