A new series of transparent aerogels of biopolymer-polysiloxane double networks is reported. Biopolymer aerogels have attracted much attention from green and sustainable aspects but suffered from strong hydrophilicity and difficulty to make homogeneous structures in nanoscale; these drawbacks are overcome by compositing with a polysiloxane network. Alginate-polymethylsilsesquioxane aerogel has high optical transparency, water repellency, comparable superinsulation property and improved bending flexibility compared to pure polymethylsilsesquioxane aerogel. The nanoscale homogeneity is realized by separating the crosslinking steps for two networks in a sequential protocol: condensation of siloxane bonds and metal-crosslinking of biopolymer. The crosslinking order, biopolymer-first or siloxane-first, and universality/limitation of biopolymer-crosslinker pairs are discussed to construct fundamental chemistry of double network systems for their further application potentials.