SummaryAllozyme and mitochondrial DNA analyses were conducted on adult workers of 319 Apis mellifera colonies from 24 Colombian localities. A high frequency of the Mdh-1 F variant (85 to 96%) was observed in all but samples from Boyacá, where a high frequency of variant M (68%) was found. An altitudinal cline of the Mdh-1 alleles was observed, with a significant increase in the frequency of M and decrease of F variants with increasing altitude. This clinal distribution suggests selective pressure on the allozymes determined by this locus. Mitochondrial DNA analysis of the 16S and COI-COII regions revealed that Colombian Apis mellifera populations are mostly made up of the African haplotype (87%). Eight RFLP COI-COII patterns were observed, six of them of the African type (A1, A4, A26, A28, A29 and A30) and two (C1 and C2) associated with the A. m. ligustica pattern. Our results indicate a strong introgression of African genotypes into the Colombian populations, as has been seen in northern Brazilian honey bees.