One underexplored dimension of allopolyploid evolution is cytonuclear interactions. Potential stoichiometric disruption caused by merging two nuclear genomes but only inheriting one set of progenitor organellar genomes (usually the maternal) suggests that cytonuclear accommodation is a necessary aspect of allopolyploid evolution. Our exploration of cytonuclear accommodation in allotetraploids of Gossypium has contributed initial understanding about how nuclear homoeologous genes (from both parental diploid species) encoding component subunits of one protein complex have evolved in the context of having their counterpart subunits encoded by genes from only one (the maternal) parent. The model protein complex we utilized is Rubisco (Ribulose 1,5-bisphosphate carboxylase/oxygenase), an essential enzyme in carbon fixation during photosynthesis, encoded by a nuclear rbcS multigene family and a single plastid rbcL gene. In Gossypium, we demonstrated their cytonuclear coordination at both genomic level and the transcriptional level. Further analysis in other angiosperm polyploid systems are being carried out to ask whether the coordination mechanisms are commonly employed by different polyploid lineages in plant kingdom (see Gong et al. citations on publication page).