Africanized honey bees entered California in 1994 but few accounts of their northward expansion or their frequency relative to European honey bees have been published. We used mitochondrial markers and morphometric analysis to determine the prevalence of Africanized honeybees in San Diego County and their current northward progress in California, west of the Sierra Nevada crest. The northernmost African mitotypes detected were approximately 40 km south of Sacramento in California's central valley. In San Diego County, 65% of foraging honey bee workers carry the African mitochondria and the estimated percentage of Africanized workers using morphological measurements is similar (61%). There was no correlation between mitotype and morphology in San Diego County suggesting these Africanized bees result from bidirectional hybridization. Seventy percent of feral hives, but only 13% of managed hives, sampled in San Diego County carried the African mitotype indicating that a large fraction of foraging workers in both urban and rural San Diego County are feral. We also found a single nucleotide polymorphism at the DNA barcode locus COI that distinguishes European and African mitotypes. The utility of this marker was confirmed using the worldwide Barcode of Life Database. Future censuses could determine whether the current range of the Africanized form is stable and the environmental factors that may underlie it.