We assessed the occurrence of Vibrio pathogens in the final effluents of a rural wastewater treatment facility in the Eastern Cape Province of South Africa as free or plankton-associated (180 μm, 60 μm and 20 μm plankton sizes) entities using standard culture-based and molecular techniques. The free-living Vibrio densities varied from 0 to 3.45 × 101 cfu ml-1, while the plankton-associated Vibrio densities vary with plankton sizes as follows: 180 μm (0-4.50 × 103 cfu ml-1); 60 μm (0-4.86 × 103 cfu ml-1); 20 μm (0-1.9 × 105 cfu ml-1). The seasonal variations in the Vibrio densities in the 180 and 60 μm plankton size samples were significant (p < 0.05), while the 20 μm plankton size and free-living Vibrio densities were not. Molecular confirmation of the presumptive vibrios isolates revealed fluvialis (36.5%), as the predominant species, followed by Vibrio vulnificus (34.6%), and Vibrio parahaemolyticus (23.1%); only API 20NE was employed to detect Vibrio metschnikovii (5.8%), suggesting a high incidence of pathogenic Vibrio species in the final effluent of the rural wastewater facility. Analysis suggested that the concentration of Vibrio species correlated negatively with salinity and temperature (p < 0.001 and p < 0.002 respectively) as well as with pH and turbidity (p < 0.001) in the final effluent. We conclude that rural wastewater treatment facilities in the Eastern Cape Province of South Africa are potential sources of Vibrio pathogens in the aquatic environment of the communities. © 2009 Elsevier Masson SAS. All rights reserved.