During the present study 80 samples of kareish (semi-soft cheese with 20% fats) and soft cheese (40 % fats) were collected Assiut City during June to December 2015. The fungal content of these samples was evaluated using Dichloran Rose Bengal Chloramphenicol (DRBC) and Yeast Extract Malt extract (YM) agar media. The fungal count per sample ranged from 7 colonies/g in soft cheese to 44800 colonies/g in kareish cheese. the total number of fungal species in kareish cheese was slightly lower on DRBC than on YM (24 and 29 species respectively). The number of fungal species per sample fluctuated between 1-8 species with the highest being recovered from kareish cheese. Aspergillus was the most prevalent genus contaminating 45-85 % of the samples with the highest being recovered from Kareish Cheese. Penicillium came next contaminating 20-47.5% of samples with white soft cheese being the most affected product. Candida, Clavispora, Klyveromyces and Pichia contaminated 2.5-65 % of samples and the highest incidence was that of Clavispora in kareish cheese. Aspergillus niger, A. fumigatus, A. flavus, Penicillium chrysogenum, P. aurantiogriseum and P. brevicompactum were the commonest species in cheese samples. Some yeast fungi were identified by sequencing of rRNA gene. Among the 19 species of yeasts Candida tropicalis, Clavispora lusitaniae, Pichia kudriavzevii, Pichia membranifaciens and kluyveromyces lactis were the most common. Testing the natural occurrence of aflatoxins revealed that AFM1 contaminated 55% and 50 % of kareish and soft cheese respectively whereas AFM2 was found only in 10 % of kareish cheese samples.