Red tilapia (Oreochromis spp.) is a valuable fish due to its uniform red skin, the absence of black peritoneum, fast growth and adaptability to any culture system, and it has a huge market in many parts of the world, such as China, Malaysia and Thailand. However, the skin color differentiation in genetic breeding and skin color variation (whole pink to black) during the overwintering period are the main problems limiting the development of commercial red tilapia culture. MicroRNAs (miRNAs) play important roles in biological processes by regulating specific gene expression. Limited microRNA (miRNA) information is available on skin color variation in fish so far. In this study, a high-throughput Illumina sequencing of sRNAs was conducted on two color varieties of red tilapia during the overwintering. The two skin color varieties were normal whole pink (WP) and pink to black color (PB). A mean of 14 748 358 and 12 981 453 raw reads from WP and PB groups, respectively, corresponded to 12 190 544 and 11 891 890 clean reads. We summarized the length distribution of all samples and found that the peak length was 22 nt. A total of 669 mature miRNAs were identified, including 337 known miRNAs and 332 novel miRNAs. Moreover, we identified 26 significant differential expression miRNAs in PB compared with WP group, including 11 up-regulated miRNAs and 15 down-regulated miRNAs. And 12 known miRNAs, i.e. miR-203a, miR-200a, miR-200b, miR-725, miR-10544, miR-204a, miR-429b, miR-129, miR-10581c, miR-10581a, miR-217 and miR-499 may play an important role in the skin color variation of red tilapia during overwintering. Enrichment analysis found many pathways related to metabolic and skin color regulation including oocyte meiosis, Wnt, Notch, calcium, Apelin signaling pathway and so on. These results would provide a basis for exploring the mechanism of skin color variation of red tilapia during overwintering.