Green fluorescent protein (GFPuv) has been widely used as a reporter fused to individual targeting sequences. However, its state in liquid and its effect on other proteins are still unclear. The conformational polymorphisms of glutathione-S-transferase-green fluorescent protein (GST-GFPuv), GFPuv and GST were analyzed by native polyacrylamide gel, indicating that GST was in many different states while GFPuv and GST-GFPuv were only in four and two slightly different states. Four different circular dichroism spectra were obtained from the GFPuv polymorphisms. The single molecular behavior of GST-GFPuv and GFPuv was also characterized by MALDI-TOF MS. Thus, we demonstrated that: (1) there might be four different structural polymorphisms for the native GFPuv; (2) GFPuv could reduce its partner's polymorphism as a fusion protein. Although GFPuv had many merits as a reporter, its unreliability was found in the study. DOI: 10.1134/S0026893311060045