Background: Candida species have an unstable resistance to common antifungal drugs. The treatment of oral candidiasis requires the identification of new anti-Candida agents with no side effects like medicinal plants. Objectives: The present study aims to investigate the antifungal effects of caspofungin and oregano essential oil on oral Candida species isolated from cancer patients. Methods: Seventy-three Candida species were identified and isolated by conventional and microbiological tests from cancer patients (n = 100) suspected of oral candidiasis. The minimum inhibitory concentrations (MICs) of the oregano essential oil and caspofungin were determined by microdilution assay and evaluated according to the Clinical and Laboratory Standards Institute (CLSI-2017). The gene regions of samples were studied using the polymerase chain reaction (PCR) method. Results: Candida glabrata (35, 47.9%) was the predominant species. Most of the Candida strains were isolated from patients with stomach cancer (35, 47.9%). The highest resistance to caspofungin was reported for C. albicans (5.5%). Also, FKS mutant isolates were associated with resistance to caspofungin. MIC90 value for oregano essential oil against C. albicans was 4096 µL/mL, which was equal to MIC90 value against C. glabrata. There was a significant difference between the MICs of caspofungin and oregano essential oil, that inhibits the growth of Candida isolates. Conclusions: The results of this study showed that the caspofungin has high antifungal effect on Candida species, specially non-albicans Candida. As the findings indicated, the oregano had good anti-Candida potent. Therefore, we could hope to treat fungal diseases by producing an appropriate herbal medicine.