Wheat is the heterogenous polyploid plant with large chromosomes and high level of repetitive sequences. These characters have limited the progress of wheat genomics studies. Comparative genomics provided a platform for study of wheat genomics by using model plants Functional genomics focused on the expressed portion of the wheat genome. Its aim was determining the expression and function of genes. This paper reviews the application of comparative genomics in wheat genomic studies and the contents and methods of functional genomics of wheat.