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Viral infections impose a great threat to backyard chicken production among poor rural households in developing countries. These infections limit the contribution of chicken production in improving the livelihoods of poor communities, particularly in Africa. Chicken viral infections lack treatment options; control and prevention depend primarily on adoption of vaccines and good farm management practice such as the institution of biosecurity measures. In backyard production systems, these control options are less practical and less feasible to implement. Research has demonstrated the role of genetic diversity of farmed animals and birds in explaining variation in resistance to infectious diseases and suggests that heterogeneous populations are less susceptible to disease than homogeneous populations. Local African chicken ecotypes have high genetic diversity and have demonstrated the ability to survive persistent exposure to pathogens and harsh environmental conditions. This suggests that local African chickens have the genetic potential to enhance breeding strategies for resistance to viral infections. Despite the ongoing threat of infectious disease and dynamic of diseases epidemiology attributed by climate change, little has been done to harness the genetic potential of local African chicken ecotypes to breed for resistant traits. To lay the foundation for future research, this review paper presents a summary of challenges facing current chicken viral infections control and prevention options in local African chickens, and gives an overview of documented information on the genetic diversity and population structure of local African chicken ecotypes.