Several cyanobacterial species, including Cyanothece sp. ATCC 51142, remarkably have four isoforms of α‐glucan branching enzymes (BEs). Based on their primary structures, they are classified into glycoside hydrolase (GH) family 13 (BE1, BE2 and BE3) or family 57 (GH57 BE). In the present study, GH13‐type BEs from Cyanothece sp. ATCC 51142 (BE1, BE2 and BE3) have been overexpressed in Escherichia coli and biochemically characterized. The recombinant BE1 was crystallized by the hanging‐drop vapour‐diffusion method. Crystals of BE1 were obtained at 293 K in the presence of 0.2 M Mg2+, 7–10%(w/v) ethanol, 0.1 M HEPES–NaOH pH 7.2–7.9. The crystals belonged to the tetragonal space group P41212, with unit‐cell parameters a = b = 133.75, c = 185.90 Å, and diffracted to beyond 1.85 Å resolution. Matthews coefficient calculations suggested that the crystals of BE1 contained two molecules in the asymmetric unit.