Sourdough fermentation is carried out by the microbial communities developed in the sourdough. Microbial species and microbial relative abundance play a major role in modulating the final product’s characteristics and ultimately, its nutritional value. In this context, we studied the microbial communities of 13 Sourdoughs collected from different geographic locations in Greece. Characterization of bacterial communities was performed through sequencing of the 16S rRNA gene. Yeast community composition was characterized through sequencing of the ITS spacer. Bacterial communities were shown to be dominated by representatives of Lactobacillus genus in all samples. In particular, L. brevis, L. pontis and L. paralimentarius dominated the bacterial communities at the Species level. Yeast communities consisted almost exclusively of Saccharomyces cerevisiae (over 97.7% of relative abundance in all samples). Alpha-diversity analysis revealed that within each sample bacterial communities were more diverse than yeast communities. Study of the microbial communities in Sourdough can help us identify the organisms that confer the desirable characteristics to the final product, thus giving us the opportunity to exploit these organisms, in order to create novel products with improved quality and nutritional value, better organoleptic characteristics (e.g. texture, palatability) and longer shelf life.