Candida is a genus of pathogenic yeast, which is one of the prevalent causes of fungal infections. While non-invasive yeast infections such as oral or vaginal candidiasis are common and can be treated with topical antifungals, invasive candidiasis in the bloodstream or internal organs can lead to hospitalisation, intensive care facilities, and aggressive medication with intravenous antifungal agents. Drug efflux ABC transporters of the most common cause of yeast infection Candida albicans (CalbCDR1), and a newly emerging Candida auris (CaCDR1) share sequence homology, that are known to play a role in multi-antifungal drug resistance. Structural investigation of CalbCDR1 and CaCDR1 would be a vital step to advance our knowledge of their function and the mechanism behind observed multi-drug resistance. However, the challenging nature of the purification of membrane proteins should not be ignored. Here, we successfully assembled mTurquoise2 fusion CalbCDR1 and CaCDR1 expression vectors via multi-fragment gap repair assembly and over-expressed in Saccharomyces cerevisiae. The expression level was measured via whole-cell and in-gel fluorescence analysis. Detergents were screened using Fluorescence-detection size-exclusion chromatography (FSEC) and their melting points (Tm) were determined using mTurquoise2 thermal assay in presence of ATP analogue AMP-PNP and triazole class of antifungal drug, fluconazole. Once the best detergent condition is established, structural studies can be performed using Cryo-EM. Furthermore, the study provides a biophysical insight into how the efflux ABC transporters of Candida species interact with the substrate and the triazole antifungal-drug molecules.