Fluorescence bioimaging is an inevitable method for biological, medical and pharmaceutical sciences to visualize substances in biological objects in a highly sensitive, multicolor and dynamic way. Recently, elongation of the fluorescence wavelength is a trend used in this imaging to suppress scattering, which limits the imaging depth to within several millimeters. It has been known that the so-called "biological window" with low loss for a biological tissue has been known to lie in the near-infrared (NIR) wavelength range between 1000 and 1700 nm. The use of fluorescence in the over-1000-nm (OTN) NIR can deepen the observation to several centimeters. The use of imaging devices based on semiconductor silicon has limited the wavelength of the fluorescence bioimaging to less than 1000 nm. However, the appearance of InGaAs CCD on the market, to allow for imaging of the OTN-NIR light, is now changing the situation. On the other hand, rare-earth doped ceramic nanophosphors (RED-CNP) can emit efficient fluorescence in the OTN-NIR wavelength range. The author's group has applied the RED-CNP to OTN-NIR fluorescence bioimaging by hybridizing the RED-CNP with various polymers or molecules. The present paper will review the development of the materials and systems for this OTN-NIR fluorescence bioimaging, together with some applications of the imaging method for biological research and a medical surgery.