FUNGI play a very treacherous role in the biodeterioration of stone monuments, leading to their loss. In order to preserve these monuments, the incidence and the biodeterioration effect of fungi on ancient limestone monuments at different Egyptian sites were evaluated. Specimens as well as swabs were collected from different Egyptian sites including, Seti Ι tomb at Luxor, Senusret Ι obelisk of Al Mattaryia district, Giza pyramid complex and related tomb, storehouse of National Museum of Egyptian Civilization (NMEC), Mosque of Judge Abd El Basset (Gamaliya), Roman Amphitheatre of Alexandria and Ismailia Museum of Antiquities. Seti Ι tomb, Mosque of judge Abd El basset and Senusret Ι obelisk were the most sites occupied by fungi, while Giza pyramid complex and Museum of Ismailia Antiquities were the lowest ones. Aspergillus niger and A. terreus were the most common and dominant fungal deteriogens of all archaeological sites, followed by Cladosporium cladosporidis, C. hebarum and A. fumigatus. Cladosporium herbarum showed the highest stone dissolution value, 23.3%, followed by A. terreus and A. niger (21.7% and 20.7%, respectively). Stone cubes incubated for two months with C. herbarum showed different aspects of deterioration including discoloration, dark pigmentation, powdering and dissolution. Also compressive strength and stone porosity were reduced by 27.7% and 25.7%, respectively. Synthetic antimicrobials; PCMC, certrimonium and TEAB inhibited all stone colonizing fungal isolates at concentrations of 1.25g/L, 5g/L and 2.5g/L, respectively, while natural antimicrobials; cinnamon, thyme and clove oil inhibited fungal isolates at concentrations of 5g/L, 5g/L and 10g/L, respectively.