Thymoquinone (TQ) is one of the bioactive constituents of black cumin seed (Nigella sativa L.) oil. It is well known that this natural volatile quinone has remarkable antimicrobial effects, especially against Candida species. Consequently, in this present study TQ was evaluated for its anticandidal effects against 14 different pathogenic Candida strains by using the in vitro, partly modified, microdilution CLSI M27-A2 method. After TQ treatment at the minimum inhibitory concentration (MIC), ultra-thin sections of C. albicans cells were thoroughly evaluated by transmission electron microscopy (TEM). The mode of action of TQ on different Candida cells was elaborated, where their disintegration and disorganization with amorphous nucleus were observed microscopically.