Abstract: Abstract：Polyacrylamide gel electrophoresis(PAGE) of seed water-soluble protein, seed salt-soluble protein, seed alcohol-soluble protein and alkali-solube protein were carried out by using 14 green, white and Guangxi wild cultivars in this experiment. At the same time, quantitative genetic distances were calculated by using 8 quantitative characters. Cluster anysis were conducted for the experiment data. The results showed that Guangxi wild bitter gourd was significantly different from other 13 cultivated cultivars in the protein fingerprints and quantitative genetic distances. However, The protein fingerprints showed a little differences among other 13 cultivars.Guangxi wild bitter gourd was regarded as a different subspecies from other 13 cultivars because of a larger genetic distance.All cultivars could not be clearly classified for the little difference.