The North of Romania is known for its wooden churches dating from the seventeenth and eighteenth centuries. Their deterioration constitutes a major problem due to their value for the cultural heritage. The microbial community from a seventeenth-century wooden church (Nicula, Romania) was investigated by characterization of uncultivated and cultivated bacteria using 16S rDNA sequence analysis. The study revealed not only the prevalence of the Bacillus thuringiensis strain IAM 12077 but also the presence of new microbial communities of Planomicrobium and Variovorax that were not previously reported in paintings or on wood. The identification of fungi showed the presence of seven common genera found on the walls and icon surfaces. Common bacteria from the human oral microbiota were not identified in the bacterial community.