Teeth and oral cavity harbor diverse community of fungi and bacteria. Little is known about fungal community of oral cavity, teeth and gingiva. In this study, fungal diversity in various sites was evaluated using Sabouraud dextrose agar (SDA). Sixty swabs samples from patients suffering from gingivitis, periodontitis and dental caries in addition to healthy persons as control (15 each) were collected for fungal analyses. Thirteen fungal species related to 7 genera were isolated and identified. To the best of our knowledge, Candida ciferrii and Cryptococcus laurentii were recorded for the first time from the oral cavity in the current study. There is a highly significant variation in the frequency of Aspergillus niger and Candida ciferrii among isolated fungi. Screening of the yeast isolates for extra-cellular enzymes production resulted in 47.2% (34 out of 72 isolates) of the tested isolates showed positive lipolytic activities with varying capabilities; whereas 41 isolates (56.9%) were positive protease producers. Also, the antimicrobial activity of some toothpastes, mouth washes, natural oils and pharmaceutical preparations against yeast species were performed. Among the tested substances, Paradontax, Hexitol and Clove oil showed the best antimicrobial activity against the tested yeast isolates. The minimum inhibition concentration (MICs) of Hexitol was high compared to Paradontax and Clove oil. This study provided clear image about fungal content in mouth, teeth and gingiva, the relation of these fungi in case of health or disease was also discussed.