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Polyploidy is an important process in plant evolution, most often involving the merger of two divergent nuclear genomes (allopolyploidy). Allopolyploidy typically is followed by genomic, genetic and epigenetic responses. Because usually only the maternal set of plastid and mitochondrial genomes are inherited in allopolyploid species, the question arises as to how plants deal with the resulting alterations to cytonuclear stoichiometry. A second understudied dimension of allopolyploid concerns small RNAs and the pace and pattern of their divergence among diploid species and following polyploidy. In this thesis I present analyses addressing these fundamental questions about allopolyploid evolution, using as models both cotton and other exemplar allopolyploid lineages.