Technical Abstract: The Hessian fly (Mayetiola destructor) is an important insect pest of wheat and an experimental organism for studies of plant-insect interactions. It has tractable genetics, polytene chromosomes, a relatively small genome (158 Mb), and shares a gene-for-gene relationship with wheat. To improve its capacity as a model plant-gall forming insect, an FPC-based genome wide physical map of the Hessian fly was constructed and anchored to the polytene chromosomes of the insect. Bacterial artificial chromosome (BAC) clones corresponding to 10.5-fold coverage of the Hessian fly genome were fingerprinted, using high-resolution capillary polyacrylamide gel electrophoresis, and end sequenced. The reliability of the FPC assembly was tested using fluorescence in situ hybridization (FISH) to co-localize two BAC clones from each of the 196 longest contigs on the polytene chromosomes. To assess contig distribution, 70 additional contigs were FISH mapped. The FISH mapped contigs were evenly distributed and covered 60% of the genome (95,668 kb). Only 3.63% of the BAC-end sequence was composed of transposable elements, helicases, ribosomal repeats, simple sequence repeats, and sequences of low complexity. However, 14.51% of the BES was comprised of multi-copy gene sequences. This physical map provides the foundation for high-resolution genetic mapping, map-based cloning, and assembly of complete genome sequencing data. The Hessian fly BAC clone assembly, and the names and positions of the BAC clones used in the FISH experiments are freely available at http://genome.purdue.edu/WebAGCoL/Hfly/WebFPC/.