The scholars of the Fundamentals of Jurisprudence, usually before defining the Fundamentals of Jurisprudence and stating the subject, put forward a discussion about the subject matter of science and consequently the criterion for unity or differences among sciences. Although the distinction and differences among sciences is an established fact, there are differences of opinion about the nature of the factors that distinguish them from each other. There are three important theories about the criterion for the distinction or unity among sciences: A) the theory prevalent among the predecessors and the logicians who tied the differences among sciences with their subject matters; B) the theory of Akhund Khorasani, who maintained that the sciences can be distinguished from each other by their objectives and purposes; C) Imam Khomeini’s theory, who maintained that the criterion for the unity or distinction among sciences lies in the compatibility latent in the essence of their problems. Describing Imam Khomeini’s viewpoints in details, attempts have been made in this article to study different aspects of his viewpoints. Employing descriptive-analytical method, the findings of this study indicate that compatibility among the problems of sciences is a corollary of the compatibility of their subject matters. Hence, compatibility-centered scientology is not an appropriate criterion for explaining the unity or differences among sciences.