Water is life and has a profound effect on human health. Vibrio cholerae is autochthonous in aquatic environment and is an important human waterborne pathogen causing cholera. This study was designed to determine the presence of Vibrio cholerae in some water sources in Zaria, Nigeria. A total of 207 water samples were collected from various water sources located in Sabon Gari and Zaria Local Government Area of Kaduna State and cultured on thiosulphate citrate bile saltsucrose agar with prior enrichment on alkaline peptone water. Presumptive isolates were identified and characterized using both conventional biochemical method and identification kit. Isolates were serotyped using Vibrio cholerae antisera kit and confirmed by PCR to detect presence of rfbO1, rfbO139 and ompW genes. Overall, V. choleraewas predominant in river (33.3%) followed by well (4.9%) and least predominant in street vended water (2.7%). None was isolated from borehole and pipe borne water. Water samples from SabonGari were most contaminated with an occurrence of 3.2% followed by Samaru (2.6%) while the least contaminated water samples were from Zaria city (1.5%). V. cholerae of the non O1/ non O139 serogroup were isolated from well, river and street vended water with a prevalence of 2.4% in Zaria. Results of this study suggest that the use of PCR targeting ompW species specific gene of V. cholerae in combination with the conventional method would be an important tool in proper identification of V. cholerae.