Degradation of plant remains is important in carbon and nutrient cycling. Next to fungi, the major wood debris decomposers, decaying wood is also colonized by bacteria. However, the relation between bacterial and fungal composition during wood decay is not yet well understood. Nevertheless, complex interactions between those two groups are expected. However, so far, limited information are available on fungal effects on the bacterial community composition in wood decay under natural conditions. The focus of the study is on bacterial community composition fluctuations in progressing pine wood decay. Comprehensive assessment of decaying pine wood inhabiting microbial communities was performed applying fungal ITS and bacterial 16S rDNA regions targeting pyrosequencing.