In this article, we review recent progress in the rapidly developing area of biomolecular interaction detection with excellent selectivity and ultrahigh sensitivity, such as DNA-DNA hybridization, DNA-protein interaction, protein function, and cellular activity, using FET-based biosensors based on the carbon nanomaterials single-walled carbon nanotubes (SWNTs) and graphenes. We also summarize some current challenges the scientific community is facing, including device-to-device heterogeneity and the lack of system integration for uniform device array mass-production.