Native fowl populations in South Africa were characterized genetically and phenotypically. Four South African native populations, two dual-purpose breeds, and two populations from Mozambique and Botswana were included for genetic analysis. For phenotypic characterization, two commercial lines were also included as a benchmark. Twenty-three micro satellite markers were selected and tested to obtain genetic data for estimation of genetic variability and distance. Growth (weight gain) and egg production were included for phenotypic characterization. A relatively high (53% ¬64%) genetic variation was found among the populations, which suggests conservation as a genetic resource for future use. The lowest genetic variation (53%) was found for the Koekoek and Australorp populations, which are the two populations that were subjected to formal selection, while the highest variation was observed in the Naked Neck population (64%). The New Hampshire has often been included in upgrading programs and this is evident from the close relationship with both the Lebowa- Venda and Naked Neck fowls. Phenotypic trials indicated significant differences among the populations included for growth, carcass and egg production traits. The Koekoek and New Hampshire populations had the best performance for egg production and growth (weight gain) in the study. Genetic and phenotypic differences indicate that the populations can be distinguished as different breeds or groups of fowl. The results of this study may contribute to selection for improved performance for household food production, as well as conservation of the populations as a genetic resource.