A cultivation-independent approach was used to identify potentially nitrogen-fixing endophytes in seven sweet potato varieties collected in Uganda and Kenya. Nitrogenase reductase genes (nifH) were amplified by PCR, and amplicons were cloned in Escherichia coli. Clones were grouped by restriction fragment length polymorphism analysis, and representative nifH genes were sequenced. The resulting sequences had high homologies to nitrogenase reductases from alpha-, beta-, and gamma-Proteobacteria and low G+C Gram positives, however, about 50% of the sequences derived from rhizobia. Several highly similar or even identical nitrogenase reductase sequences clustering with different bacterial genera and species, including Sinorhizobium meliloti, Rhizobium sp. NGR234, Rhizobium etli, Klebsiella pneumoniae, and Paenibacillus odorifer, could be detected in different plants grown in distinct geographic locations. This suggests that these bacterial species preferentially colonize African sweet potato as endophytes and that the diazotrophic, endophytic microflora is determined only to a low degree by the plant genotype or the soil microflora.