Long non-coding RNA (lncRNA) is a type of RNA with a length of over 200 nucleotides that can interact with DNA, RNA, or proteins to regulate target genes at the transcriptional, post-transcriptional, and epigenetic levels. Based on the previous transcriptome sequencing data of Cyprinus carpio var. koi skin tissues, we screened four lncRNAs that were significantly differentially expressed in three skin tissues (black, red and white). In order to further explore the function of these lncRNAs in skin color differentiation and synthesis, a preliminary study of the relationship between their functions and miRNAs was also conducted. Firstly, the 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 was 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 those 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. These findings suggest that lncRNA172145 could be involved in the regulation of the melanogenesis pathway by targeting to miR-206, providing the fundamental information for further research into the specific molecular mechanisms of their roles in the melanogenesis pathway, as well as the role of long non-coding RNAs in regulating fish body pigmentation and differentiation.