Universally Primed-PCR (UP-PCR) and Internal Transcribed Spacer-PCR (ITS-PCR) based genomic fingerprinting techniques are considered a good methods that rely on specifically targeted primers. These techniques, which analyse the rDNA, have been shown to be relatively robust and discriminatory. This study was designed to investigate and characterize the molecular variation among Cladosporium strains collected at different sites in Cairo by using two different fingerprinting methods, Universally Primed-PCR (UP-PCR) and Internal Transcribed Spacer (UP-PCR) technique. The Cladosporium isolates investigated were isolated from air of Cairo by settle plate method. The samples were then purified and identified by using culture based techniques, microscopical methods, and biochemical reactions followed by confirmation in the regional center for mycology and biotechnology (RCMB). Molecular fingerprinting, and genetic similarities among Cladosporium species populations depending on microsatellites-polymerase chain reaction (ITS-PCR). Primers used are ITS4, and ITS5. PCR products were digested with 3 restriction enzymes and separated by agarose electrophoresis. Restriction patterns generated by CfoI, MspI and RsaI. In addition, we have applied the Universally Primed PCR (UP-PCR) technique using two primers L21 and Fok1.The current work showed prominent discriminatory power given by amplification of internal transcribes spacers PCR regions followed by restriction with CfoI enzyme than other endonucleases. moreover, Fok1 primer revealed minor variability among Cladosporium strains using UP-PCR genotyping technique.