The aim of this study was to establish phenotypic and genetic diversities of Candida species isolated from women with recurrent Candida vaginitis. A total of 3000 samples were cultured from 3000 women with and without complaints of vaginal discharges and pruritis vulvae. Growth characteristics on Sabouraud's dextrose agar and on conidia enhancing media (Corn meal agar) resulted in isolation of 5440 distinct colonies of Candida species. They were then analyzed by germ tube test to separate C. albicans from non-albicans Candida species. For confirmation, 300 doubtful isolates were then tested on API 20C AUX and by polymerase chain reaction.The results showed Candida albicans species to be dominant 3661 (67.29%) while non-albicans Candida species presented only 1779 (32.71%) which included C. glabrata 435(8.0%), C. tropicalis 762(14.0%), C. krusei 163(3.0%), C. famata 109(2.0%), C. parapsilosis 131(2.41%), C. guilliermondii and C. lusitaniae each 27(0.5%) respectively, C. incospicua 13 (0.24%), C. norvegensis 82(1.5%), C. colliculosa 16 (0.3%) and C. magnoliae 15 (0.27%). On genotypic diversity, the principle coordinate analysis of the PCR results for the genetic relatedness and genetic distances revealed the distribution of 200 isolates tested as: C. albicans 90(36%), C. glabrata 40(20%), C. krusei 20 (10%), C. tropicalis 20 (10%), C. famata 10(5%), C. parapsilosis 5(2.5%), C. norvegensis 6(3%), C. lusitaniae 4(2%), and C. guilliermondii 5(2.5%).From this study it shows that a combination of biochemical methods and PCR technology may identify most of the isolates, including the germ tube negative isolates. Both symptomatic and asymptomatic women possessed similar species and genotypic diversities. However, in symptomatic women, a single host can be colonized with multiple species or multiple Journal of Biology and Life Science ISSN 2157-6076 2013 www.macrothink.org/jbls 154 genotypes of the same species. In order to establish if the same species behave differently in symptomatic and asymptomatic individuals, this study recommend further investigation on virulent factors.