Abstract: This paper describes the characteristic of isozyme patterns of peroxidase, esterase, and acid phosphatase of Pinus yunnanensis; P. kesiya var. langbianensis, and P. yunnanensis var, pygmaea during their seeds germination. The species differences among the three kinds of seeds were clear in each typical isozyme pattern. But the isoperoxidase patterns changed with the increasing of germination days of seeds, so it is difficult to determine the isoperoxidase patterns of these seeds. The isozyme patterns of esterase and acid phosphatase were relatively steady, and there were more specific isozyme banks in these seeds than in those of the isoperoxidase pattern, so it is easy to determine these two kinds of isozyme patterns. The isozyme patterns of esterase and acid phosphatase may be considered as the physiological index to differentiate these three kinds of seeds which were very similar in the morphology. Besides the above, the application of isozyme pattern similarity to the study of the relationship between these species and their evolution were also discussed.