A method of producing functional molecule-containing silica nanoparticles on which a biomolecule is bonded, containing the steps of: allowing silica nanoparticles containing a functional molecule and having a thiol group on a surface thereof to coexist with a linker molecule having a maleimido group and a carboxyl group in an aprotic solvent, thereby allowing formation of a thioether bond between the thiol group and the maleimido group, and obtaining functional molecule-containing silica nanoparticles on which the linker molecule is bonded; and allowing the functional molecule-containing silica nanoparticles on which the linker molecule is bonded to coexist with carbodiimide and a biomolecule having an amino group in an aqueous solvent, thereby allowing formation of an amide bond between the carboxyl group active esterified by the carbodiimide, and the amino group of the biomolecule.