DNA computing is a branch of biomolecular computing using the physical and chemical properties of deoxyribonucleic acid or DNA. It is a fast-developing interdisciplinary research area consisting of nano-biotechnology, computer science and biochemistry. DNA computing is widely used now-a-days for logic design, biomarker, cryptography, disease detection etc. In recent years, carbon nanotube or CNT research has reached a new peak with its various applications including nano-biocomputing. DNA plays a pivotal role in biology and CNT is considered as a wonder material of this century in nanoscience. This chapter combines these two promising research areas including CNT and DNA to form CNT-DNA based nanostructured system and its applications in diverse fields like electronics, biomedical engineering, drug delivery, gene therapy, biosensor technology etc. CNT-DNA hybrid and its various suitable combinations open up a new dimension called CNT-DNA computing.