In order to comprehensively address the mechanism responsible for the pigment pattern formation in the skin of marble and brown trout, different cellular and genetic approaches were applied. The related species have a different skin pigment pattern, marble trout expressing a unique labyrinthine, while brown trout has a spot pattern. Pigment cell ultrastructure and their position in the skin were examined with TEM. In the brown trout skin, we found erythrophores (type 1 and type 2), which were not found in the skin of the marble trout and were described here for the first time. The pigment cell organization in the skin of brown trout is more organised, compared to that in marble trout. Based on our findings, we couldn’t find a connection between a position of specific pigment cell type and different pigment pattern in the skin. Transcriptomes of cells from differently pigmented regions, obtained by cryosections from the region where chromatophores are located, were sequenced using NGS. The results have shown a large set of differently expressed transcripts between species, but also between differently pigmented regions. Among these transcripts, there were several coding for membrane proteins, which are involved in cell-cell communication. The red dot in brown trout had a unique expression profile, this region is the only one containing the type 2 erythrophore. Using qPCR, we examined the expression of 22 candidate genes on a larger number of samples. The expression of six of these genes was tested in hybrids between the two species. The genes p21, gja5 and tjp1 were displaying the highest correlation between their expression level and skin pattern. Based on our results, we can conclude that specific cell-cell communication (gap junctions, tight junctions, channels et. al.) between pigment cells is responsible for the pattern formation in trout.