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Agile manufacturing is the main mode of global manufacturing in 21st century. The basic organizational form of it is dynamic alliance. As a new type of strategy for optimization and integration of enterprises' external resources, dynamic alliance is becoming an important component of many corporations' strategy. The selection of partners plays an important role in the foundation of dynamic alliance. The method based on fuzzy integral evaluation and rough set theory is effective to evaluate the partners. Fuzzy integral evaluation has been of great help in managing subjective judgment, and rough set theory is prevailing in managing the objective historical data. This paper presents a comprehensive evaluation method based on fuzzy integral evaluation method and rough set theory to evaluate partners. The conclusions which are more up to practice can be drawn by synthesizing the two algorithms.