Cowpea is an important food and fodder legume in the sub-humid tropics of Africa, with Nigeria being its largest producer at 2.58 +/- 0.31 million metric tonnes per year. Although cowpea has the ability to fix nitrogen with broad range of rhizobia it has been reported to respond positively to inoculation with specific strains. Biological nitrogen fixation is important in providing nitrogen to the growing cowpea and can contribute to better soil fertility. Given the problems of low soil fertility and high fertilizer costs, the development of cheap rhizobia inoculant may be a promising alternative for resource-poor smallholder’s farmers in Sub-Saharan Africa. This study aims to explain observed differences in inoculation response in cowpea and to explore the potential benefits of rhizobium inoculation. The roles of the abundance and community structure of compatible rhizobia in determining inoculation response in different soils will be determined and their potential determinants identified by analysis of soil chemistry and cultivation history. Based on these results, a set of effective and competitive indigenous rhizobium strains will be identified to be tested for their potential as commercial inoculants.