| Based on the transcriptome sequencing data of Cyprinus carpio var. koi skin tissues in the previous research, four lncRNAs were screened that were significantly differentially expressed in the three skin types (black, red, and white); and target binding sites between lncRNA172145 and miR-206 in the melanogenesis pathway were identified through RNAhybrid and TargetScan target gene tools. Then, the coding ability of lncRNA172145 was detected by CPC, CPAT, and CNIT software, and the results confirmed that this sequence is lncRNA with no protein coding ability. The temporal and spatial expression levels of this sequence were further analyzed by qRT-PCR, and it was demonstrated that the levels were significantly higher in the eyes, black skin, fins and blood than that in other tissues; and the expression levels started to increase significantly from the gastrulation stage, and the high-level trend continued until 20 days after hatching. Additionally, with the help of dual luciferase reporter assay, the existence of a targeted regulatory relationship between lncRNA172145 and miR-206 was further verified. Finally, miR-206 was silenced in vivo by synthesizing miR-206 antagonist, and the results showed that the expression level of lncRNA172145 in the miR-206 antagonist group, was significantly higher compared to the negative control antagonist group and the PBS group. This study suggests that lncRNA172145 may be involved in the regulation of melanogenesis pathway by targeting to miR-206, which provides fundamental information for the subsequent in-depth investigation of the specific molecular mechanisms of them in the regulation of skin color.