The first decade of the 21st century has been labeled as "the sensing decade". The functional nanomaterials offer excellent platforms for fabrication of sensitive biosensing devices, including optical and electronic biosensors. A lot of works have focused on the biofunctionalization of different nanomaterials, such as metal nanoparticles, semiconductor nanoparticles and carbon nanostructures, by physical adsorption, electrostatic binding, specific recognition or covalent coupling. These biofunctionalized nanomaterials can be used as catalysts, electronic conductors, optical emitters, carriers or tracers to obtain the amplified detection signal and the stabilized recognition probes or biosensing interface. The designed signal amplification strategies have greatly promoted the development of stable, specific, selective and sensitive biosensors in different fields. This review introduces some novel principles and detection strategies in the area of biosensing, based on functional nanomaterials. The general methods for biofunctionalization of nanomaterials with biomolecules and their biosensing application in immunoassay of protein, DNA detection, carbohydrate analysis and cytosensing are also described.