-Africanized honey bees (AHBs Apis mellifera) have been reported in NW Mexico since the mid 90s, but no study on the process of admixture with local European honey bees has been conducted. Morphometrics and haplotype analyses were used to investigate the frequency of African markers in honey bees from Sonora (SON), the north and south of Baja California (BCN and BCS). Morphometrics identified 42% of the samples from SON, 44% from BCN and 15% of BCS as Africanized. Honey bees from BCS had larger body size and formed a separate cluster from BCN and SON which were similar to each other. The molecular analysis revealed a higher frequency of African-derived haplotypes in SON (48%) and BCN (50%) compared to BCS (21%). The morphometric and molecular evidence suggests that the colonization of BCS by AHBs may be recent. Nest and food availability in desert areas and beekeeping practices are evoked to explain the reduced introgression of African genes into honey bee populations from this region of Mexico.Apis mellifera / Africanized honey bee / Baja California / hybridization / haplotype / morphometrics