In this study, mycological examination were conducted on different samples from human, animals and poultry in El-Fayoum and Beni-Suef governorates, Egypt in the period from January to June 2013. The antifungal activities of thyme, clove and cinnamon oils against the recovered fungal isolates were tested using agar dilution method. A total of 209 samples were collected (including vaginal swabs from 18 women, 82 cows and 9 buffaloes beside 100 swabs from broiler chickens; 20 crops and 80 proventriculus). Eighty nine fungal isolates were recovered (40 mold and 49 yeast isolates). Eleven (61.1%) fungal isolates were recovered from women; of which 1 isolate was A. flavus and 10 were Candida species while 39 (42.9%) fungal isolates were recovered from animals; of which 36 were molds and 3 were C. albicans. In broiler chickens, 39 (39%) fungal isolates were recovered; of which 36 were yeast; 34 Candida species and 2 Cryptococcus species and 3 were molds; 2 A. niger and 1 A. flavus. PCR assay using oligonucleotide primer that amplifying 172bp fragment in SAP3 gene of C. albicans confirmed morphological, biochemical and biological identification of C. albicans. The antifungal activities of the tested essential oils against the recovered fungi revealed that thyme oil completely inhibited the growth of different fungal isolates at concentrations of 0.25, 0.5 and 1%. Clove and cinnamon oils completely inhibited the growth of different fungal isolates at a concentration of 6%.