WRKY transcription factors are important molecules in regulating plant development and resistance. Recently, the sequenced Arabidopsis lyrata genome allows us to characterize the number and structure of WRKY genes in this species. A total of 71 AlWRKY factors were classified into the previously defined polyphyletic WRKY groups I to III. The exon/intron structure and motif compositions of WRKYs were highly conserved in each group, but tended to be different between groups and species. The WRKY family has a set of genes similar to that in A. thaliana, but in Populus trichocarpa this family has expanded significantly, except for the subgroup III genes. Segmental duplication and gene conversion events have played important roles during the evolution of the WRKY gene family in the three species. Especially, the gene expansion events differentiated in WRKY subgroups during the evolution, and we have detected positive selection in several sites of the group III genes. In addition, this subgroup was the most structurally diversified in the WRKY family. Our study demonstrated that the group III members of WRKY gene families in A. lyrata, A. thaliana, and P. trichocarpa have experienced different selection pressure during the process of evolution and this may have played a vital role in plant adaptation.