Background Pregnant women are susceptible to vaginal candidiasis and maternal vulvovaginal candidiasis is a major risk factor for colonization and/or infection of the infant. The purpose of this study was to determine the prevalence and antifungal patterns of albicans and non-albicans Candida among pregnant women attending a tertiary referral hospital. Methods Vaginal discharge- cotton swabs were self-collected from pregnant women clinically proven to have vulvovaginal candidiasis at the antenatal clinic of a tertiary referral hospital between January and July 2018. Microscopy and culture on Sabouraud's Dextrose Agar with chloramphenicol was done on the vaginal discharge-cotton swabs. Confirmatory fungal identification was done using CHROM agarTM Candida. Antifungal susceptibility testing was carried out using the standardized Kirby Bauer dilution method. Results Candida were isolated from 50.81% (126/249) of the swabs and included C. albicans (80.16%, 101/126), C. glabrata (19.05% (24/126) and C. krusei (0.79%, 1/126). Of the women from whom Candida were isolated, 11.1% (14/126) were in the first trimester, 39.7% (50/126) were in the second, while 49.2% (62/126) were in the third. Of the Candida isolates, 80.16% (101/126) were C. albicans, 19.05% (24/126) were C. glabrata and 0.79% (1/126) were C. krusei. Overall, all the isolates were non-susceptible to Amphotericin B, while 60.3% (76/126), 50% (63/126), 62.7% (79/126), and 48.4% (61/126) were non-susceptible to itraconazole, fluconazole, nystatin, and clotrimazole respectively. All the non-albicans Candida were resistant to itraconazole, amphotericin B, and fluconazole. Conclusion Vulvovaginal candidiasis due to multidrug resistant C.glabrata among pregnant women will require that treatment regimes are adjusted to carter for the recurrent forms. The use of CHROMagarTMCandida media for identification of clinically relevant Candida should be adopted instead of conventional methods that are tedious and time consuming such that treatment is based on laboratory evidence.