Two genes encoding starch branching enzyme II (SBEII) have been identified in apple. These genes share 94 and 92% identity in coding DNA sequences and amino acid sequences, respectively; moreover, they have similar expression patterns. Both genes are expressed in vegetative and reproductive tissues, including leaves, buds, flowers, and fruits. Based on genomic Southern blots, there are two copies of SbeII genes in the apple genome. Comparisons of genomic sequences between monocots and eudicots have revealed that the genomic structure of SbeII genes is conserved. However, the 5'-terminal region of coding DNA sequences of SbeII genes shows greater divergence than the 3'-terminal region between monocots and eudicots. Phylogenetic analysis of DNA sequences has demonstrated that the duplication patterns of SbeII genes are different between monocots and eudicots. In monocots, the duplication of SbeII genes must have occurred prior to the radiation of grasses (Poaceae); while, in eudicots, the expansion of SbeII genes must have followed the process of speciation.