Candidiasis infection is caused by different species of Candida, which are characterized by host immunologic weakness. Black cumin seeds (Nigella sativa) have shown an inhibitory effect against Candida albicans. In this work, the inhibitory effect of standardized extract and different fractions of Nigella sativa seeds has been evaluated on both nystatin-susceptible and resistant strain of C. albicans. Canadida albicans (NSCA) with ATCC 76645 and nystatin-resistant Candida albicans (NRCA) were prepared from oral samples of HIV individuals. Total extract and different fractions of N. sativa were prepared using maceration and sonication methods. Thymoquinone (TQ) content of the plant was determined by spectrophotometric method. Total extract (TTE) and the fractions along with TQ were evaluated on NSCA and NRCA by the microdilution method. TQ content of the plant was 0.92 ± 0.37g/100g dried extract. The least MIC and MFC (62.5 and 125 μg/ml, respectively) were due to petroleum ether fraction (PEF) against both NSCA and NRCA, followed by chloroform fraction (CHF) with MIC and MFC of 125 and 250 μg/ml, respectively. TQ exhibited MIC of 0.78 and 3.12 μg/ml against NSCA and NRCA, stronger than nystatin (MIC of 2 and 16 μg/ml, respectively). Thymoquinone was detected in the PEF and CHF. Considering more inhibitory effects of PEF and CHF than TTE, we can conclude that active components of the plant belong to non-polar compounds. PEF showed identical inhibitory effects on NRCA and NSCA, which is a valuable result for finding novel medicaments against NRCA infections.