Abstract: Since Darwin and the earliest theory of population genetics, it has been well known that breeding system plays an important role in genetic diversity and evolution of organisms. After elucidation of the rationale for the use of protein electrophoresis in assesment of breeding system of plants, experimental results obtained by Chinese and foreign scientists has been cited. Although many characters of plants such as life form, mode of reproduction etc. do influence genetic structure of populations, the most significant matter is the relationship between breeding system and population genetic differentiation. Since that we can make a deduction from breeding system to population genetic structure, and further to sample strategies which are critically important to monitoring genetic diversity of in situ conservation and ex situ conservation.