Polyploidy has long been recognized as an important force in the evolution of flowering plants and often results in novel phenotypes having advantages in adaptation and major interest for agriculture. Many crops, including citrus, are bred to a higher level of ploidy in search of desirable traits. In previous works of our group synthetic clementines with different levels of ploidy, specifically haploid, dihaploid and autotetraploid, were generated. This plant material represents a valuable tool for studying the effects of polyploidization at the molecular level since important traits are expressed in different manners. By using a microarray approach, we have accomplished a comprehensive analysis of transcriptome divergence among the newly created clementine lineages with different genome dosage. Differences in expression in the bark tissue of the four lineages were found significant for 89 (haploid-dihaploid comparison) or 93 genes (diploid-tetrapolid comparison). These genes were classified on the basis of their structure in different families.