A new organic–inorganic hybrid synthesized through a sol-gel process starting from alkoxysilane and chitosan is reported. Functionalization of the hybrid was effected through in situ hydrolysis–condensation reaction of methyltrimethoxysilane (MTMS) and vinyltrimethoxysilane (VTMS) in the reaction medium. The process yields highly transparent and hydrophobic silica–chitosan hybrids. The hybrid gel was investigated with respect to chemical modification, thermal degradation, hydrophobicity, and transparency under the ultraviolet-visible region. The extent of hydrophobicity had been tailored by varying the precursor ratio. SiO2–chitosan–MTMS hybrids showed a higher thermal stability than SiO2–chitosan–VTMS (SCV) hybrids with respect to hydrophobicity. Condensation of silsesquioxanes generated from the hydrolysis of MTMS and VTMS over the silica-chitosan particles impart hydrophobicity to the hybrid. The coatings of functionalized SiO2–chitosan precursor sol on glass substrates showed nearly 100% optical transmittance in the visible region. The present hybrid material may find application in optics and other industries.