Allopolyploidy, a common and ongoing phenomenon among angiosperms, entails hybridization coupled with whole-genome duplication, and produces new species containing two or more homoeologous subgenomes. Allopolyploidy has major effects on plant genome structure and gene expression patterns, which can cause novel phenotypes not observed in progenitors. Allopolyploids often experience subgenome dominance, the preferential expression of homeologs from one of the two progenitor genomes (subgenomes). To better understand the immediate and long-term consequences of allopolyploidy and the extent to which subgenome dominance is a legacy of the progenitors’ expression patterns, we investigate global gene expression architecture and the fate of homeologs in Nicotiana (Solanaceae). Nicotiana is an ideal system for studying alloployploid evolution because of extensive genetic and genomic resources and because half of Nicotiana species are allopolyploids of different ages. We focus on gene expression in Nicotiana section Repandae, including three allotetraploid species, N. nudicaulis, N. repanda, and N. stocktonii, derived from hybridization between N. sylvestris and N. obtusifolia ~4.3 million years ago. We identify genes with differential expression across tetraploid and diploid species, as well as across stages of corolla development within each species. Furthermore, we investigate subgenome dominance patterns to track the homeolog expression bias in allopolyploids. Finally, we explore expression patterns of potential candidate genes for underlying variation in flower size. We find clear expression differences between the two progenitor species, with all the allopolyploids intermediate between them.  We observe a slight bias toward N. obtusifolia, especially in the leaf tissues. Hierarchical clustering based on differential expression across corolla developmental stages reveals similar common expression patterns and different numbers of transcripts in various species. We also see differential expression of several known flower size candidate genes across the corolla developmental stages. Collectively, these results provide a perspective on evolutionarily persistent expression alterations after allopolyploidization and hint at the underlying genetic basis of speciation events.