Nucleic acid sequence of a gene is an important property as it carries the identity of an organism. Molecular methods are based on the detection of the nucleic acid sequence of a gene specific to an organism. In probe-based identification, the organisms single stranded DNA or RNA would bind to a complementary sequence and form hybrid which is double stranded. Identification of specific organisms can be done from the clinical specimen, culture, formalin-fixed or paraffin-embedded tissues ( Hong, 2006 ). The use of rRNAs is essential for probe-based detection of species as its nucleotide sequence is well conserved within a species and varies between species. Therefore, it is used as a target for species identification. Sequencing the amplified regions of Internal Transcriber Spacer regions (ITS) of the rRNA gene for Candida gained success in species identification ( White et al ., 1990 ). The early discoveries were in C. dubliniensis ( Sullivan et al ., 1995 ), C. orthopsilosis and C. metapsilosis ( Tavanti et al ., 2005 ) using PCR methods. In Denmark, differentiation between C. orthopsilosis and C. metapsilosis was performed using a newly described RFLP method using SADH (secondary dehydrogenase-encoding gene), 26S rRNA (D1/D2) and ITS1-ITS2 regions ( Mirhendi et al ., 2010 ). In another study, molecular identification using ITS1-ITS4 fungal primers were able to identify C. orthopsilosis which was previously identified as C. parapsilosis with API 20C test kit ( Yong et al ., 2006 ). Very recently, a rapid real-time PCR method was also developed to distinguish C. metapsilosis , C. orthopsilosis and C. parapsilosis . Different melting curve used was able to identify the three species mentioned above. Hays et al . (2011) and Gomez-Lopez et al . (2010) reported that a strain which was identified as C. kefyr with biochemical test method was discovered to be C. sphaerica by ITS sequencing. In another report, strains of C. haemulonii was mis-identified as C. sake , Pichia ohmeri and other Candida spp. by biochemical test kits ( Ruan et al ., 2009 ). However, molecular methods revealed their species identity. A multiplex PCR method used in another study was able to differentiate C. nivariensis and C. bracarensis which are phenotypically identical to C. glabrata ( Romeo et al ., 2009 ).