Optical labelling reagents (dyes and fluorophores) are an essential component of probe-based biomolecule detection, an approach widely employed in a variety of areas including environmental analysis, disease diagnostics, pharmaceutical screening, and proteomic and genomic studies. Recently, functional nanomaterials, as a new generation of high-value optical labels, have been applied to molecular detection. The great potential of such recent optical labels has paved the way for the development of new biomolecule assays with unprecedented analytical performance characteristics, related to sensitivity, multiplexing capability, sample throughput, cost-effectiveness and ease of use. This review aims to provide an overview of recent advances using different nanoparticles (such as quantum dots, rare earth doped nanoparticles or gold nanoparticles) for analytical genomics and proteomics, with particular emphasis on the outlook for different strategies of using nanoparticles for bioimaging and quantitative bioanalytical applications, as well as possibilities and limitations of nanoparticles in such a growing field.