Invasive candidiasis and aspergillosis are amongst major medical concerns with high mortality among immunocompromised patients. Management of these infections is dependent on early and efficient antifungal therapy, as well as drug resistance monitoring. Decreased sensitivity of these pathogens to antifungal drugs during recent decades calls for rapid detection/identification of drug resistance associated mutations in pathogenic fungal species. Generally, a study for identification of drug resistance associated mutations requires complicated and expensive methods such as PCR or sequencing.  However, nowadays application of accurate, fast and highly sensitive techniques, including Rolling Circle Amplification (RCA), PCR-RFLP, Real-Time PCR, and ARMS-PCR provide the possibility for detection of target sequence containing nucleotide polymorphisms even at the one base pair level. In this review we aimed to discuss the usage, advantages and disadvantages of these techniques in order to identify the mutations of the azole-resistant strains.