Our research paid attention to molecular evolution and structure of KsgA/Dim1 family in cyanobacteria,which catalyzes the dimethylations of two neighboring adenines in small ribosomal subunit rRNA. The phylogenetic analysis of 16S rDNA and ksgA gene from MEGA 5.2 showed evolutionary conservation of KsgA/Dim1 family in cyanobacteria. The homology model of KsgA protein constructed by SWISS-MODEL indicated that the fold of KsgA of cyanobacteria is two-domain architecture and relatively well conserved. The functional complementation assay was used to express KsgA from cyanobacteria Synechocystis sp. strain PCC 6803, Anabaena sp. strain PCC 7120 and Synechococcus elongates sp. strain PCC 7942 in Escherichia coli mutant to detect dimethyltransferase activity. The results indicated that the functions of E. coli ksgA mutanats was complemented by cyanobacteria ksgA to some extent.