Nanomaterials possess several useful properties, including large surface-to-volume ratio, high biocompatibility, facile surface modification and overall structural robustness. They also have unique optical, magnetic and electronic properties. Nucleic acids, whether designed or selected in vitro, play important roles in biological assays and clinical diagnostics. In addition to nucleic acid probe-based nucleotide complementarity, aptamers, which can bind with high affinity and specificity to a wide range of target molecules, comprise a new class of nucleic acids selected in vitro. The coupling of nucleic acids, including aptamers, with various nanomaterials provides special opportunities for developing novel biosensing systems with advanced and powerful functions. This review summarizes recent achievements in the design of nucleic acid-functionalized nanomaterials for bioimaging applications, especially carbon nanomaterials, gold nanoparticles, semiconductor nanoparticles, magnetic nanoparticles, and polyacrylamide nanoparticles. Because DNA is easier to synthesize and more stable than RNA, this review mainly focuses on the bioimaging applications of DNA-functionalized nanomaterials.