One of the well-studied components of the insect gut is the peritrophic matrix (PM). This semipermeable structure primarily functions in digestion, and protection against invasive microorganisms and mechanical damage. We report the cDNA cloning and transcription profiles of a peritrophin-A like gene (designated MdesPERI-A1) in the Hessian fly Mayetiola destructor. The predicted amino acid sequence of MdesPERI-A1 revealed a putative secretion signal peptide at its amino terminus, similarity to peritrophins from other insects including dipterans, and the presence of two chitin binding domains each containing six cysteine residues. Quantitative expression analysis of MdesPERI-A1 mRNA in different larval tissues revealed the transcript to be predominantly present in the midgut (597.9-fold) compared to other tissues assayed including salivary glands and fat bodies. Spatial expression patterns during development showed a peak expression of MdesPERI-A1 in the feeding second-instars (146-fold) and a decline in expression in the pupal and adult stages. Transcription profiling of MdesPERI-A1 during compatible (larvae on susceptible plants) and incompatible (larvae on resistant plants) interactions with wheat revealed a greater level (1.7-fold) of MdesPERI-A1 transcript in larvae on resistant plants in the initial time point examined. However, MdesPERI-A1 expression declined in larvae on resistant plants at the later time points.