The freeze-drying of anionic megamolecules extracted from gelatinous cyanobacteria, Aphanothece sacrum, formed spongy materials capable of metal adsorption to form hydrogels. Cryogenic-transmission electron microscopy demonstrated that thicker nanofibers were formed in sacran/In3+ complexes than in sacran/Sn4+. The preferential sorption of In3+ into the hydrogels occurred in the mixed solution of In3+ and Sn4+ with concentrations below 40 mM. Since In3+ was condensed in the sponges, electrolytic refinement of indium was made using the ion-complex hydrogels at room temperature to obtain indium metal foil at a pure grade over 99.9%. Furthermore, the sponges were recovered and used again, to successfully obtain highly pure indium metal, in even the second and third trials. Thus epochal energy-saving methods for indium refinement were established using spongy hydrogels of cyanobacterial polyanions.