Recent advances in high-throughput DNA sequencing and other genomics tools have greatly increased the ability and precision of gene characterization, even in plant species with large, complex genomes such as tobacco. A blue mold resistance (BMR) locus originating from Nicotiana debneyi has been deployed in several commercial burley varieties. This source of resistance has been underutilized, however, due to a yield penalty associated with plants that are homozygous at this locus, and an observed reduced efficacy when the locus is heterozygous. We subjected near-isogenic burley lines that differ at the BMR locus, as well as an accession of N. debneyi, to RNA-seq analysis to identify genes of N. debneyi origin that are located on the foreign introgression region in the blue mold resistant burley isoline. Given that introgression fragments derived from wild Nicotiana species frequently fail to recombine with their N. tabacum genomic counterparts, an additional objective involved testing whether recombination was actively occurring within the chromosomal region that contains the BMR locus. Our results showed that this region is recombinationally active, meaning that it should be possible to reduce the size of the introgression fragment, and likely reduce the associated yield drag, while retaining the BMR trait. The results of the RNA-seq analyses will discussed within the context of our strategy to produce superior blue mold resistant tobacco cultivars.