AbstractA few queens of the honeybee, Apis mellifera scutellata, were imported from Africa and released in Brazil in 1957. Progeny of these bees have now largely colonized the American tropics. Their imminent arrival in the United States poses a serious threat to the beekeeping industry and to agriculture dependent on honeybee pollination. African and European bees are morphologically very similar. DNA restriction fragment length polymorphisms are proving successful in distinguishing between the two. Several DNA markers specific to European honeybees have been described previously. Reported here are three cloned honeybee DNA probes that reveal polymorphisms that appear to be either African or European specific. Of fourteen alleles or haplotypes identified, five were present only in African and neotropical (Venezuelan and Mexican) African bees but absent in European‐derived bees, two were present only in European‐derived bees but absent in samples from South Africa. Another allele showed apparent frequency differences among populations. Such markers are useful in studying the genetics of neotropical African bee populations. Venezuelan and Mexican honeybee colonies show a preponderance of the African alleles with low levels of the European alleles. These observations of nuclear DNA, revealing limited paternal European introgression, together with previous mitochondrial DNA findings showing negligible European maternal gene flow into feral African populations, indicate that neotropical African bees are primarily African.