It is widely accepted that green plants evolved the capacity to synthesize the highly organized branched alpha-polyglucan amylopectin with tandem-cluster structure, whereas animals and bacteria continued to produce random branched glycogen. Although most previous studies documented that cyanobacteria accumulate glycogen, the present study shows explicitly that some cyanobacteria such as Cyanobacterium sp. MBIC10216, Myxosarcina burmensis and Synechococcus sp. BG043511 had distinct alpha-polyglucans, which were designated as semi-amylopectin. The semi-amylopectin was intermediate between rice amylopectin and typical cyanobacterial glycogen in terms of chain length distribution, molecular size and length of the most abundant alpha-1,4-chain. It was also found that Cyanobacterium sp. MBIC10216 had no amylose-type component in its alpha-polyglucans. The evolutionary aspect of the structure of alpha-polyglucan is discussed in relation to the phylogenetic evolutionary tree of 16S rRNA sequences of cyanobacteria.