Magnetic iron oxide nanoparticles functionalized with 4-carboxyphenylboronic acid (CPBA-MNPs) were developed for extracting genomic DNA, total RNA and nucleic acids from seeds. The seed samples were genetically-modified maize seeds and unmodified soybean seeds infected by bean pod mottle virus and tobacco ringspot virus. The total nucleic acids, genomic DNA, and RNA could be separately extracted from these seeds with high qualities using CPBA-MNPs under different conditions. Furthermore, the results of real-time quantitative qPCR and real-time reverse transcription (RT)-PCR indicated that the nucleic acids extracted from these seeds using CPBA-MNPs were suitable for the detection of genetically-modified seeds and seed-borne viruses.