This study aimed to evaluate the incidence of fungi in soft skimmed milk cheese through manufacturing of soft skimmed milk cheese from pasteurized milk and trial to control them by application of some substances (chitosan, natamycin and thym oil) which known to have antifungal activity to milk during manufacturing. Seventy-five soft skimmed milk cheese samples were collected randomly from supermarkets, groceries, small dairies and street-vendors at Gharbia Governorate for mycological examination. In addition, soft skimmed milk cheese was manufactured from pasteurized milk in lab with addition of natamycin (0.02%, 0.015%), chitosan (1.5%, 1%) and thyme oil (1.5%, 1%) and check the quality of cheeses during storage period. The obtained results revealed that 36% of examined samples were contaminated with mould with a mean count of 4.4x103±6.8x102cfu/g. The profile of the genera and species of mould isolated from soft skimmed milk cheese samples were A. flavus 8 (32%), Penicillium spp 14 (56%) P. decumbens 7 (50%), P.citrinum 2 (14.3%), P. coryphilum 2(14.3%), and P. concentricum 3(21.4%). Byssochlamys nivea 3 (12%), while 68% of examined soft skimmed milk cheese samples were contaminated with yeast with a mean count of 1.8x104 ± 2.6x103cfu/g.The frequency distribution of yeast isolated from the examined soft skimmed milk cheese samples were Candida 22.2%, Rhodotorulla 19.5%, Saccharomyces 13.8%, Debromyces hansenii 19.5%, Yarrowia lipolytica 2.8% and Torulopsis 22.2%. The results of this study showed that manufactured cheese containing natamycin and chitosan had better effect on organoleptic properties and total mould count than cheese containing thyme oil.