Due to the low photostability of conventional organic fluorophores, their effectiveness in detecting proteins in highly autofluorescent cyanobacterial cells is limited. However, the inorganic fluorescent nanocrystal (Quantum Dot or Qdot) conjugates have the capability to overcome the limitation of organic fluorophores, and provide a promising tool for long-term imaging studies. In this study, we applied Qdot conjugated secondary antibodies associated with specific primary antibodies, and successfully detected nitrogenase and IdiA proteins in situ in highly autofluorescent cyanobacterial cells of the unicellular Crocosphaera watsonii (WH8501) and the non-heterocystous Trichodesmium erythraeum (IMS101).