Molecular data have had a profound effect on the field of plant evolutionary biology, yet the potential wealth of data stored in low-copy nuclear-encoded genes has been virtually ignored, relative to studies of chloroplast and ribosomal DNA. In this dissertation I present an analysis of a model nuclear-encoded gene family (alcohol dehydrogenase, Adh) in a model organismal system, the cotton genus (Gossypium L., Malvaceae);A combination of PCR- and Southern hybridization-based approaches was employed to isolate, sequence, and map multiple Adh gene family members. Diploid Gossypium contain at least seven Adh loci. Sequence analysis reveals extensive intron variation between loci, and one locus has lost two introns. Evolutionary rates differ between loci and between lineages. Finally, the Adh gene family appears dynamic in that examples of gene duplication, pseudogenization, and elimination were found;We have also employed Adh genes for phylogenetic analyses. We tested the relative utility of seven noncoding cpDNA regions and a pair of homoeologous nuclear genes for resolving recent divergences, using tetraploid cottons as a model system. We sequenced over 7 kb of CPDNA per taxon, yet obtained incomplete phylogenetic resolution. We also sequenced a 1.65-kb region of a homoeologous pair of Adh genes and obtained a robust and completely resolved topology. This enhanced resolution reflects an approximately three- to six-fold increase in evolutionary rate relative to the cpDNA sequences;Finally we have exploited Adh sequences to study intraspecific genetic diversity. We estimated nucleotide diversity for a pair of homoeologous Adh loci in allotetraploid G. hirsutum. Nucleotide diversity for AdhA in Gossypium is lower than for any plant nuclear gene yet described. This low diversity appears to reflect a history severe genetic bottlenecks supplemented by an unusually slow nucleotide substitution rate and an autogamous breeding system. While not statistically supportable, the sum of the observations also suggest differential evolutionary dynamics at each of the homoeologous loci.