This study investigated the microflora of ancient trees growing around two historical monuments in Samarkand city — the Ulugbek Observatory and the Sherdor Madrasah. The morphological characteristics of pure cultures of microorganisms isolated from the collected samples were examined. The results showed that 21 micromycete and 16 bacterial isolates were obtained from trees near the Ulugbek Observatory, and 17 micromycete and 16 bacterial isolates from trees near the Sherdor Madrasah. Analysis of the microbiome composition revealed the presence of pathogenic and potentially harmful species that may affect the trees and nearby historical monuments.