Microbial diversity in historical monuments and their role in the destructive processesis a problem ofgreatinterest. Different groupsofmicroorganisms could be a part of this negative effect. Lower Egypt abounds in important cultural remains (tombs and mosques) and special attention is required for their protection. Fungi are involved significantly in deterioration of Egyptian tombs and mosques to the East and West of the Nile Delta. The present study is focused on biodiversity of contaminant fungi from different materials in these historical monuments. A total of 30 isolates were obtained from the analyses of 13 samples taken from different tombs in Egypt. Isolated strains were identified using ITS region and the SSU ribosomal RNA gene sequencing. The dominant genuses among isolates were Pencillium and Aspergillus. This study is a first report on the taxonomy of fungi inhabiting the mentioned part of world cultural heritage. The chemical composition of pigments and limestone was also investigated. Current results are a summarized study of fungal strains from seven monuments and can be included in conservation methods development.