The principle of yeast two-hybrid were summarized, the basis for large scale yeast two-hybrid screening of protein-protein interaction was given and the main application of yeast two-hybrid in large scale screening of protein-protein interaction was presented. The problems of large scale yeast two-hybrid screening of protein-protein interaction were also discussed. Because there were a lot of false positives and false negatives in the result of protein-protein interaction obtained by large-scale yeast two-hybrid screening, the employment of other methods to study protein-protein interaction in large scale in parallel was proposed if possible.