In order to determine the function of pigment cell types in different pigment pattern of skin, we have applied the laser capture microdissection method (LCM) for isolation of different pigment cell types from skin sections of marble trout (Salmo marmoratus) and brown trout (S. trutta), characterized with labyrinthine and spotted skin pattern, respectively. RNA was isolated from dissected pigment cell populations and used for expression analysis. Expression profiles of candidate genes, potentially involved in pigmentation, in LCM isolated pigment cell population, were more specific compared to differently pigmented skin regions, containing a heterogeneous mixture of cells, including more types of chromatophores. Moreover, they could provide important information about particular pigment cell type function and its contribution to different pigment pattern. Protocol of combined LCM and genomic approach to study single pigment cell populations can be applied in the future, but needs to be further optimized in order to yield RNA of sufficient quantity and quality required for i.e. transcriptomic analyses.