In current time, invasive fungal infections have become a major threat for the immunocompromised hospitalised patients. Also, healthy individuals are much prone to the commensal yeasts of the oral cavity. Different surveys and studies have recorded increased rate of Candida albicans and non-albicans such as of C. glabrata, C. tropicalis, C. guilliermondii, C. dubliniensis, C. parapsilosis and C. krusei in local and systemic fungal infections. Thus, a rapid and correct identification of different Candida species plays an important role in diagnosis and antifungal therapy against candidiasis. The conventional diagnostic methods, such as histopathology and culture which are based on morphological and physiological attributes are low in sensitivity and also not very accurate. Development and standardisation of various molecular techniques (both PCR and non-PCR based) have proved to be promising approach for correct and quicker identification of Candida species. More and more technical development in these methods can bring their widespread clinical use with much more ease in coming days. The purpose of this review is to highlight the value, limitations and current state of different molecular approaches utilized for species level identification in Candida diagnostics.