Approaches for the discovery of protein-coding genes were described in detail in Chap. 3. These included EST sequencing, RNA-seq, and full genome sequencing. Raw DNA sequences generated by these approaches are assembled into sets that are assumed to come from a single genetic locus. These are often called unigene sets. Currently, it is believed that there may be as many as 50,000 unique genes (unigenes) in conifer genomes, although this number will likely decline as more sequence data and better bioinformatics tools reveal that the number of unigenes has been overestimated. This can result from allelic or alternative splicing differences at a single locus. In this chapter, our goal is to discuss what is known about the structure (introns, exons, promoters, other regulatory regions) of conifer genes and their relationship to one another in gene families. The discussion is organized around functional classes of genes that have been of most interest in conifers.