We have detected a second-order nonlinear optical response from aggregates of the ampholytic megamolecular polysaccharide sacran extracted from cyanobacterial biomaterials by using optical second-harmonic-generation (SHG) microscopy. The SHG images of sacran cotton-like lump, fibers, and cast films showed SHG intensity microspots of several tens of micrometers in size. The dependence of the SHG spot intensity on an excitation light polarization angle was observed to illustrate sacran molecular orientation in these microdomains. We also observed SHG signals around a special region of the cast film edges of sacran. These results show that sacran megamolecules aggregate in several different ways.