Polyploidization instantly doubles all genome content by combining two genomes that have markedly different methylation and gene expression levels. This process may be accompanied by genetic and epigenetic changes in each genome. Sequencing of the transcriptome (RNA-seq) and the methylome (bisulfite treated libraries whole genome libraries) were used to measure gene expression and methylation levels of genic regions of allopolyploid cotton petals and petals of their diploid relatives. Many differentially expressed genes detected by RNA-seq were consistent with expression levels previously detected by microarrays. RNA-seq results also reconfirmed the presence of general polyploid gene expression trends like expression level dominance and homoeologous expression biases in Gossypium polyploid species. Expression biases between A- and D-genome homoeologs and expression level dominance was characterized for thousands of genes in tetraploids and a diploid F1-hybrid. Unlike the results of microarray study previously done we found a slightly greater number of genes showing A-genome bias vs genes showing D-genome bias. More commonly the overall expression level from homoeologs of polyploid is heterotic i.e the expression level is greater than the average of the expression levels from the two parent genomes. In addition, genome methylation (CG, CHG, and CHH contexts) of each genome was assessed in the diploid and tetraploid samples. The A- and D-genomes had distinct levels of DNA methylation for each context. DNA methylation may be independently regulating homoeologous expression levels of a small number of genes.