In the United States, few studies have been conducted on the genetic variation of honey bees, Apis mellifera L. in queen breeder colonies. In this study, a 571-572 bp region of the mitochondrial DNA (mtDNA) cytochrome oxidase I and II (COI-COII) genes was sequenced from 140 colonies from 14 queen breeders in the United States. DNA sequence analysis revealed seven different mitotypes (C1, C2, C11, C12, C19, C27, C31) from 14 queen breeders in 11 states. The most common mitotypes were C1, C2 and C11 which accounted for 82% of the observed mitotypes, while two mitotypes were singletons. Of the seven observed mitotypes, two (C27, C31) have not been previously described. The observed mitotype and nucleotide diversity was 0.74985 and 0.00352 respectively. This is the first study to use mtDNA sequences extensively on queen breeder colonies in the United States. DNA sequencing is more sensitive to genetic variation than PCR-RFLP as it detects single nucleotide polymorphisms (SNPs). Future studies using the same molecular method can also be conducted on the feral (unmanaged) population in order to understand the population genetic structure of honey bees in the United States.