Carbon-based luminescent nanomaterials have attracted much attention in the biomedical field. Compared to traditional photoluminescent materials (such as rare earth-based semiconductors and organic dyes), they have excellent biocompatibility, low toxicity, excellent optical stability and site-targeting properties in addition to their low cost and environmentally friendly features. Carbon dots, a typical carbon-based luminescent material, have great application potential in biomedicine, biological imaging and optoelectronics. Actual biological imaging, however, uses low-level photon scattering and light absorption to avoid self-fluorescence by the target tissues, requiring the light waves to have strong tissue penetration ability. Long wavelength (red and near-infrared) is known to have strong tissue penetration. However, carbon dots in the long wavelength region give a low quantum yield. Thus, obtaining long wavelength-emitting carbon dots with high quantum yield is a big challenge in practical bioimaging and phototherapy. In this paper, recent progress in the development of long wavelength, strongly luminescence-emitting carbon dots, the mechanisms and methods to regulate their optical properties and improve their quantum yield are reviewed. Recent applications of carbon dots in biosensing, bioimaging and therapy are described. Finally, the future challenges and prospects of long wavelength carbon-based luminescent materials are discussed. [GRAPHICS] .