Western capercaillie (Tetrao urogallus) are a large galliform species that inhabits mostly coniferous forests at altitudes above 1000 m.a.s.l. Over the last 60 years, a sharp decline in capercaillie populations was observed in many of central European habitats, especially at the peripheral range of the species distribution. Accordingly, recent monitoring data in Croatia indicate a 77% decrease in lek numbers. Measures aimed at recovery and restoration of the capercaillie population are complex and include a variety of factors such as habitat modelling, pest control, and the potential reintroduction or supplementation of captive bred animals. The breeding of animals in captivity may result in behavioural, morphological and health differences that may reduce post-release survival rates. The aim of this study was to analyse the faecal microbiome of captive birds from the aviary in the Gorski Kotar region (which has a more coniferous forest) with that from wild birds in Lička Plješivica (premontane beech forests) and Northern Velebit Mountain (more coniferous forests). Samples were collected from known animals in the aviary and opportunistically from wild animals, kept cold using ice packs and transported to the Veterinary Faculty. The DNA of the microbiota was isolated using a commercial kit, purified and then sent for sequencing and bioinformatic analysis to an external service. In total, 11 microbial phyla were detected with Firmicutes, Proteobacteria, Actynobacteria and Bacteroidetes being the most abundant. Juvenile animals had higher proportions of Firmicutes indicating a higher ratio of animal protein in the diet. With increasing age, proportions of Proteobacteria and Bacteroidetes increased, because of the shift to a more plant oriented diet. The richness and diversity of the microbiome was higher in samples from wild animals. The gut microbiome of captive animals was more similar to that of wild birds from Northern Velebit, indicating similar dietary conditions. By adjusting the gut microbiota according to a specific habitat, post-release survival rates and the efficiency of conservation programs should improve.