The presence and frequency of decay fungi in living Abies cilicica and Abies bornmulleriana was examined from 200 healthy-looking trees in 40 different stands in western regions of Turkey. Totally, 965 and 1059 fungal isolates were obtained from A. cilicica and A. bornmulleriana, respectively using increment bore cores. Isolates were identified by PCR amplification of the ITS region and sequencing. In addition, decay fungi were detected directly from wood samples using species-specific primers. The most abundant decay fungi isolated were Heterobasidion abietinum, Hyphodermelia rosae, Cerrena unicolor, Stereum hirsutum and Bjerkandera adusta. Heterobasidion abietinwn was mostly found in cores taken from the stem base of the trees. Multiplex PCR results yielded Stereum sp., Phellinus sp. and Ganoderma lucidum directly in DNA extracted from the bore cores. Species that are members of Ascomycota such as Cladosporum herbarum, Trichoderina sp., Phoma sp., Penicill ium sp. and Alternaria alternata were also isolated from both tree species.