Background: Candida is an opportunistic pathogen that is common in humans, especially pregnant women. The fungus is a frequent cause of oral candidiasis, candidemia, cutaneous candidiasis, systemic infections, and vaginitis with high mortality and morbidity rates globally. Although several studies have been conducted on vaginal candidiasis, there is currently no documented report of the infection in the study area. Therefore, the current study was designed to assess the prevalence, characterize Candida species (Candida spp.) with a molecular approach, and further assess the predisposing risk factors in pregnant women attending antenatal clinics in Anyigba, Kogi State, Nigeria. Method: High vaginal swab (HVS) samples were collected from 50 pregnant women between the month's May to July 2022. The sample was cultured using Sabouraud dextrose agar (SDA) and cultured, identification was carried out with morphological characteristics, germ tube test was used for further identification, and their DNA was extracted for molecular analysis. Result: Out of the 50 pregnant women sampled, 36 (72%) tested positive for Candida spp. Further identification using a germ tube test was carried out in which 12(33.33%) tested positive for Candida albicans. The age group 26-35 years had the highest prevalence rate of 16(44.44%) while 36-45 recorded the least prevalence rate of 6(16.66%). The result also showed that women in their third trimester recorded the highest prevalence rate of 22(61.11%). In terms of the effect of the level of education, there was a high prevalence at the primary level 16 (44.44%). Based on their occupation, traders recorded the highest prevalence rate of 20(55.55%) while civil servants had the least 6(16.66%). However, Internal Transcribed Spacer (ITS) gene extracted for molecular analysis revealed Candida albicans (CBS:6362; 8.33%, IMAN-25; 16.66%, IMAN-225; 8.3% and IMAN-22, 11.11%), Candida akabanensis; 27.77%, Pichia kudriazevii (Candida krusei) 16.66% and Candida glabrata (11.11%). Conclusion: Based on the observations made, there is a need for routine surveillance and education of pregnant women on Candida spp. infection as a holistic procedure in antenatal care. In addition, the use of molecular characterization will enhance the proper identification of Candida spp. in hospital settings.