Quantum dots (QDs) have received great attention for development of novel fluorescent nanoprobe with tunable colors towards the near-infrared (NIR) region because of their unique optical and electronic properties such as luminescence characteristics, wide range, continuous absorption spectra and narrow emission spectra with high light stability. Quantum dots are promising materials for biosensing and single molecular bio-imaging application due to their excellent photophysical properties such as strong brightness and resistance to photobleaching. However, the use of quantum dots in biomedical applications is limited due to their toxicity. Recently, the development of novel and safe alternative method, the bio-mediated greener approach is one of the best aspects for synthesis of quantum dots. In this Chapter, bio-mediated synthesis of quantum dots by living organisms and biomimetic systems were highlighted. Quantum dots based fluorescent probes utilizing resonance energy transfer (RET), especially Förster resonance energy transfer (FRET), bioluminescence resonance energy transfer (BRET) and chemiluminescence resonance energy transfer (CRET) to probe biological phenomena were discussed. In addition, quantum dot nanocomposites are promising ultrasensitive bioimaging probe for in vivo multicolor, multimodal, multiplex and NIR deep tissue imaging. Finally, this chapter provides a conclusion with future perspectives of this field.