The stone samples of historical monuments around Yildiz Technical University Besiktas Campus were investigated using DNA extraction-PCR-DGGE methods, scanning electron microscopy (SEM), XRF, and other analytical methods to assess stone decay over the centuries. Microbial diversity was examined by classical cultivation and modern diagnostic methods besides modern analysis techniques. The number of the microorganisms in per gram of stone samples was calculated by microbial culture methods. SEM analysis showed that stone surfaces have too many pores, decaying pieces and microbial colony. It is put forth by XRF analysis that stone materials have some elements serving the growth of microorganisms. It was concluded that there is a close connection the stone structure and microbial growth, most likely mineralogical composition, hardness and porosity of stone. Cyanobacterial microorganisms lived on stone surfaces were also determined using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments. It was revealed DNA-based molecular analysis of 16S rRNA that 23 bacterial/Cyanobacterial clones were inhabited to stone materials.