To investigate the effects of water flow on fish body color, the number of melanophore and gene expression in zebrafish skin were investigated under water flow culture with two different flow rates 0.010 m/s (low flow rate) and 0.022 m/s (high flow rate). The results showed that compared with low flow rate, the number of skin melanophore increased significantly after 3 months of culturing zebrafish under higher flow rate, especially in the caudal region of the body of the fish, the expression levels of the skin melanophore marker genes kita, mitfa and tyrp1a were significantly increased as well. Meanwhile, the relative expression level of the xanthophore marker gene csf1ra was significantly decreased, and there was no significant change in the iridophore marker gene pnp4a, indicating that the high flow rate water induced the formation of melanophore and inhibited the formation of xanthophore. The RT-qPCR results showed that the expression of melanophore formation inhibitor gene asip1 was significantly decreased in the skin of zebrafish in the high-flow group compared with that in the low-flow group； the melanocortin receptor gene mc1r and the amelanocortinogen gene pomca, which are related to melanophore formation, were not significantly changed； and the retinoid dehydrogenase genes raldh2 and raldh3, which are related to retinoic acid synthesis, were significantly down-regulated； water flow stimulation upregulated the transient receptor channel protein gene trpv4 and the piezoelectric mechanosensitive channel protein gene piezo2, whereas there was no significant change in piezo1. The above results indicate that the high flow rate water flow induces melanophore formation in zebrafish, possibly as a result of reduced asip1 expression mediated by water flow stimulation through the skin mechanosensitive proteins Trpv4 and Piezo2. Asip1 regulates fat accumulation in addition to melanophore formation, and indeed zebrafish body fullness reduces significantly in the high water flow group compared with low flow rate group. GO enrichment analysiss showed differentially expressed genes was mainly enriched to entries for triglyceride catabolism, HDL particles, lipid binding, etc and differentially expressed genes was significantly enriched in the following KEGG pathways： aminoglycan and nucleotide sugar metabolism, PPAR signaling pathway, linoleic acid metabolism, and arachidonic acid metabolism, etc. RT-qPCR showed the fatty acid peroxidase 2 gene fads2, which is associated with lipid metabolism, was significantly up-regulated, and there was no significant difference in the leptin gene lep, indicating that water flow may affect fat degradation through Asip1 affecting Fads2. In conclusion, this study for the first time reported the effect of water flow on fish body color and proposed a preliminary signaling regulatory pathway, which provides a preliminary theoretical basis for understanding the effect of water flow culture on fish body color and fullness.