In this review, we summarize recent advances in the development of molecular recognition components based on the biomolecular scaffolds of proteins and nucleic acids for specific recognition of miscellaneous targets. In addition to the widely adopted recombinant antibody fragments, designed ankyrin repeat proteins and modular peptide repeats of transcription-activator-like effectors for base-specific recognition of DNA sequence are also briefly introduced. For the nucleic acid based molecular recognition systems, aptamers, including slow off-rate modified aptamers, DNAzymes, and synthetic DNA-like oligomers for versatile biorecognition are described. Finally, we discuss the remaining challenges and future research directions in the field.