My research is focused on advancing understanding of the genomes of two important distantly related conifer species, loblolly pine (Pinus taeda L.) and bald cypress (Taxodium distichum (L.) Rich. var. distichum). Loblolly pine is the most commercially important tree crop in the United States, the major source of pulpwood for paper manufacturing, a source of quality lumber, a prime bioenergy feedstock, and an important part of the ecosystem of the southeastern U.S. Bald cypress is the dominant tree species in the aptly named ¡°cypress swamps¡± of the South.Its ecological importance to the wetlands of the southern U.S. is immeasurable. Moreover, bald cypress is a popular ornamental due to its attractive appearance and extreme resistance to pests, pathogens, and weather. Maintaining the security and productiveness of these important crop/forest species in the face of new pest, pathogen and environmental threats will require a better understanding of their genes and the structures of their genomes. We have conducted a study of loblolly pine and bald cypress in which Cot analysis and DNA sequencing of Cotiltered DNA were utilized to study genome structure. Cot analysis revealed that loblolly pine and bald cypress genomes are each composed of three major kinetic components which we have deemed highly repetitive (HR), moderately repetitive (MR), and single/low copy (SL). In loblolly pine, the HR, MR, and SL components account for 57, 24, and 10%, of genomic DNA, respectively. Of note 2.71% of random genomic sequences (i.e., 580 Mb, an amount roughly three times that of the Arabidopsis genome) show significant (bit score ≥ 60) homology to mRNA sequences. This result suggests that the loblolly pine genome contains many genes or pseudogenes, and/or gene duplications. In bald cypress, the HR, MR, and SL components account for 52, 38, and 4%, of genomic DNA, respectively. Sample sequencing was performed only on the HR component of bald cypress; sequence analysis shows only 0.81% of HR sequence reads with homology to mRNA sequences. My research provides insight into the evolution of these distant conifers and key sequence data that should greatly facilitate ongoing molecular breeding programs.