Objective The contribution of sexual transmission to genital Candida infection remains unclear. This study sought to investigate whether sexual behaviours were associated with the presence of genital Candida species among a cohort of women who have sex with women (WSW) in addition to determining the genetic concordance of genital Candida spp. among WSW in sexual partnerships. Methods WSW =18 years of age presenting to the Mississippi State Department of Health STD Clinic during 2009-2010 completed a sexual behaviour survey. Culture of vaginal fluid was performed for Candida spp. identification; associations with participant characteristics were determined using logistic regression analysis. Random amplified polymorphic DNA (RAPD) PCR was performed on DNA extracted from yeast cultures of WSW in sexual partnerships in which both partners had isolates of Candida spp. identified and among a set of age/sexual behaviour matched controls. RAPD genetic fingerprints were evaluated by hierarchical cluster analysis for concordance. Results Genital Candida spp. were isolated in 105/196 (53.6%) of women: 13/105 (12.4%) had symptomatic vulvovaginal candidiasis while 92/105 (87.6%) had asymptomatic vaginal colonisation. Bisexual identity, sex with women and men during the past 12 months and numbers of male sexual partners during the past 12 months were the only significant predictors of genital Candida spp. in bivariate analysis. 13 pairs of WSW in sexual partnerships in which both partners had genital Candida spp. and 11 WSW with genital Candida spp. not in sexual partnerships were identified. Candida spp. RAPD banding patterns were discordant for all isolates among WSW within partnerships and in controls. Conclusions This study found no evidence supporting sexual transmission of genital Candida spp. between women.