Plants being sessile organisms have developed specialized mechanisms for regulating their development as well as perceiving and responding to external signals. Most of these processes are controlled at the transcriptional level and transcription factors (TFs) play a vital role for this purpose by binding to cisregulatory elements present in promoter regions of target genes. The recent availability of complete genome sequence of diploid cotton species i.e. Gossypium raimondii and Gossypium arboreum offers an opportunity to study the evolution of WRKY and DOF TF families. Our finding predicted that segmental duplications were the principle route of expansion of DOF family in G. raimondii and G. arboreum. Only one DOF on chromosome 6 in G. arboreum was believed to be resulted from tandem duplication. Segmental duplications also seemed to be predominant for expansion of WRKY gene family in both these species. A large genomic fragment of chromosome 1 in G. arboreum containing multiple WRKY domain encoding genes seemed to be duplicated on chromosome 4 in G. arboreum. Similarly DOF genes on chromosome 2 might have duplicated on chromosome 4. A couple of DOF genes also seemed to be evolved as a result of tandem duplications on chromosome 3 and 10 in G. arboreum. On the other hand, only one DOF genes on chromosome 1 in G. raimondii was proposed to be evolved due to tandem duplication. The Gene structure analysis demonstrated the intron loss occurred during the course of evolution from CrDOF (only DOF of green algae Chlamydomonas reinhardtii) in DOF family in both these species. So the majority of DOF genes in both species were intronless, while some DOFs had single introns. Intron losses in only some of the WRKY genes were also observed. These studies would help us for the functional studies of members of these TF families in cotton.