Studies of positively selected genes (PSGs) in microorganisms and mammals have provided insights into the dynamics of genome evolution and the genetic basis of differences between species by using whole genome-wide scans. Systematic investigations and comparisons of PSGs in plants, however, are still limited. In this study, the genome sequences of two cotton species, Gossypium arboreum and G. raimondii, were compared, including whole genome duplication (WGD) events and genomic features such as gene number, gene length, codon bias index (ENC), evolutionary rate, number of expressed genes, and retention of duplicated copies. The data suggest that, unlike the PSGs in G. raimondii, G. arboreum comprised more PSGs, smaller gene size and fewer expressed gene. In addition, the PSGs evolved at a higher rate of synonymous substitutions (Ks), but were subjected to lower selection pressure (Ka/Ks). The PSGs in G. arboreum were also retained with a lower number of duplicate gene copies than G. raimondii after a single WGD event involving Gossypium. These data indicate that PSGs in G. arboreum and G. raimondii differ not only in Ka/Ks, but also in their evolutionary, structural, and expression properties, indicating that divergence of G. arboreum and G. raimondii was associated with differences in PSGs in terms of evolutionary rates, gene length, expression patterns, and WGD retention in Gossypium.