Simple SummaryThe skin mucosa in fish is equipped with innate immune mechanisms, which constitute the first line of defense against potentially harmful factors in the aquatic environment. Prebiotics, such as galactooligosaccharides (GOS), mediate modulation of the immune responses. Dietary prebiotics promote the development of intestinal microbiota, which interacts with the immune system. In this study, we analyzed the effects of the GOS prebiotic applied as a feed additive on molecular responses in the skin mucosa of the common carp. The genes analyzed encode various proteins associated with the innate immune response in skin mucosa in fish, such as mucin secretion, antimicrobial peptides, and enzymes. Modulated expression of those genes at the mRNA level regulates the defense mechanisms in the skin mucosa. In this study, supplementation with GOS increased the mRNA level of interferon and lysozyme, which are involved in fighting infection. At the same time, GOS decreased the mRNA level of CRP, which is a marker of inflammation. We conclude that supplementation with GOS modulates innate immune processes in the skin mucosa of common carp. Further studies could be focused on analyzing the effects of GOS on the microbiota composition of the skin mucosa and the mitigating effects against environmental stress.Galactooligosaccharides (GOS) are well-known immunomodulatory prebiotics. We hypothesize that GOS supplemented in feed modulates innate immune responses in the skin-associated lymphoid tissue (SALT) of common carp. The aim of this study was to determine the impact of GOS on mRNA expression of the immune-related genes in skin mucosa. During the feeding trial, the juvenile fish (bodyweight 180 ± 5 g) were fed two types of diet for 50 days: control and supplemented with 2% GOS. At the end of the trial, a subset of fish was euthanized (n = 8). Skin mucosa was collected, and RNA was extracted. Gene expression analysis was performed with RT-qPCR to determine the mRNA abundance of the genes associated with innate immune responses in SALT, i.e., acute-phase protein (CRP), antimicrobial proteins (His2Av and GGGT5L), cytokines (IL1β, IL4, IL8, IL10, and IFNγ), lectin (CLEC4M), lyzosymes (LyzC and LyzG), mucin (M5ACL), peroxidase (MPO), proteases (CTSB and CTSD), and oxidoreductase (TXNL). The geometric mean of 40s s11 and ACTB was used to normalize the data. Relative quantification of the gene expression was calculated with ∆∆Ct. GOS upregulated INFγ (p ≤ 0.05) and LyzG (p ≤ 0.05), and downregulated CRP (p ≤ 0.01). We conclude that GOS modulates innate immune responses in the skin mucosa of common carp.