The use of magnetic nanoparticles (MNPs), such as iron oxide nanoparticles (IONPs), in biomedicine is considered to be a valuable alternative to the more traditional materials due to their chemical stability, cost-effectiveness, surface functionalization, and the possibility to selectively attach and transport targeted species to the desired location under a magnetic field. One of the many main applications of MNPs is DNA separation, which enables genetic material manipulation; consequently, MNPs are used in numerous biotechnological methods, such as gene transfection and molecular recognition systems. In addition, the interaction between the surfaces of MNPs and DNA molecules and the magnetic nature of the resulting composite have facilitated the development of safe and effective gene delivery vectors to treat significant diseases, such as cancer and neurological disorders. Furthermore, the special recognition properties of nucleic acids based on the binding capacity of DNA and the magnetic behavior of the nanoparticles allowing magnetic separation and concentration of analytes have led to the development of biosensors and diagnostic assays; however, both of these applications face important challenges in terms of the improvement of selective nanocarriers and biosensing capacity. In this review, we discuss some aspects of the properties and surface functionalization of MNPs, the interactions between DNA and IONPs, the preparation of DNA nanoplatforms and their biotechnological applications, such as the magnetic separation of DNA, magnetofection, preparation of DNA vaccines, and molecular recognition tools.