A rapid and accurate identification of the Candida is crucial for clinical treatment of local and systemic candidiasis. Premature diagnosis of invasive fungal infections is problematic because most clinical signs are non-specific and cultures are often negative or become positive too late for the initiation of effective antifungal therapy. Therefore, studies have been performed to improve molecular techniques for the diagnosis of candidiasis. Today, molecular strategies, such as PCR and non-PCR based methods are used to complement conventional laboratory approach. They provide accurate results in much short time of 1.5–3 h. Given the high accuracy and time saving with molecular typing techniques it is likely that most of these methods could improve routine clinical laboratory identification of Candida yeast species. However, further studies are needed for standardization of such procedures. This article presents an overview and discussion on molecular identification methods in the context of their application for the diagnosis of Candida fungi. Particular attention has been focused on the advantages and limitations of the indicated methods and the possibilities of their implementation for routine use in clinical laboratories.