SBP-box proteins are plant-specific putative transcription factors, which contain highly conserved SBP domain and could bind specifically to promoters of the floral meristem identity gene SQUAMOSA and its orthologous genes to regulate their expressions. In this study, 17 non-redundant SBP-box genes in Arabidopsis genome and 19 in rice genome were identified by using the known SBP domain sequences as queries. The phylogenetic analysis suggested that the main characteristics of this family might have been in existence before the split of Arabidopsis and rice, and most SBP-box genes expanded in a species-specific manner after the split of monocotyledon and dicotyledon. All the SBP-box proteins were classified into 9 subgroups based on the phylogenetic tree, where each group shared similar motifs and the orders of the motifs in the same group were found almost identical. Analysis of nonsynonymous and synonymous substitution rates revealed that the SBP domain had gone through purifying selection, whereas some regions outside SBP domain had gone through positive or relaxed purifying selection. The expression patterns of the SBP-box genes were further investigated by searching against the EST database. Results showed that the Arabidopsis SBP-box genes are expressed chiefly in flowers, leaves, roots and seeds, while those in rice mainly in flowers and callus.