Human plague is found in the West Nile region of Uganda and Democratic Republic of the Congo where flea vectors are often found inhabiting homes. We have developed a multiplexed, real-time polymerase chain reaction assay targeting mitochondrial genes that is capable of detecting blood meal sources in fleas collected off-host in East Africa. Laboratory tests showed that the assay is specific for the intended targets and has a detection limit below one picogram of DNA. Testing of wild-caught fleas from the Democratic Republic of Congo suggests that humans are at significant risk from flea-borne disease and implicates domestic animals including cats, chickens, and the black rat as potential sources of human exposure to fleas and flea-borne diseases. Future application of the assay will help us better define the ecology of plague in East Africa to implement effective control measures to combat the spread of disease.