Most women suffer from severe vaginal candidiasis caused by Candida spp. Vaginal infections represent a second type of common disease. This infection occurs commonly in married and pregnant women and immunocompromised patients. This study aimed to survey, isolate and diagnose the vaginal Candida spp. using phenotypic and molecular assays. Candida isolates were recovered from patients attending main hospital in Babylon Province, Iraq from July 2011 to April 2012. Samples were subcultured on CHROMagar for preliminary identification of Candida isolates. Germ tube and chlamydospore formation were also performed to confirm identification. DNA of representative isolates was extracted for polymerase chain reaction (PCR) assays and analyzed using gel image patterns of bands for different isolates based on ultraviolet transilluminator band software. Results show that CHROMagar was a good tool for preliminary identification of Candida isolates. Molecular identification of PCR and random amplification polymorphism DNA (RAPD-PCR) assays were used to group the representative Candida isolates into different genetic patterns; phylogenetic tree was generated based on the information available in gel images. This study concludes that PCR and RAPD PCR assays confirmed more the diagnosis of Candida isolates than culture on CHROMagar medium and other phenotypic tests.