The western honey bee, Apis mellifera L., was introduced into North America over four hundred years ago. Due to the introduction of small founder populations during the settlement of the U.S., the decimation of US populations by Varroa destructor and current queen breeding practices, the amount of genetic variation present in the U.S. honey bee population needs to be characterized and quantified. Past studies using allozymes and mitochondrial DNA analysis reported measurable genetic differences between the two main queen breeding regions in the U.S. (western and southeastern United States) However; these studies were performed before major losses of bee populations occurred due to the Varroa mite. During these studies the commercial queen breeding stock was resampled, and the current genetic composition of U.S. honey bee populations is being assessed. These results are being compared to the composition of a sample set collected in 1993-1994. Mitochondrial and nuclear DNA analysis are being used to test hypotheses related to changes in genetic variability in the U.S. commercial queen breeding populations over the past decade. Microsatellite analysis is being used to assess whether commercial strains of honey bees in the U.S. retain measurable genetic affinities to their progenitor subspecies. Quantifying the genetic variability of the U.S. queen producing populations will allow us to understand the genetic heritage of the commercial strains of honey bees and to rationally address the complex issue of the need for additional germplasm importation.