The given paper deals with the problem of the relationship between religion and science as perceived through the prism of Orthodox theology in contemporary Russia. It describes both the official position of the Russian Orthodox Church concerning academic science and secular education and separate views of various Orthodox authors. The author pays particular attention to incorporation of theology into the secular sphere of academic education in the Russian Federation and discussions in the Russian Orthodox environment concerning this problem. The author notes that such an initiative of archpriest Pavel Svetlov (1841-1945) was not supported at the Pre-Conciliar Presence of 1906, although many people at that time were aware of the need for reforms of Russian Orthodox Theological Academies. On the contrary, today the Russian Orthodox Church insists on the incorporation of theological departments in all universities of the country despite protests of secular public. Obviously, contemporary theological departments in Russia according to their founders should not be just a copy of Western Christian models of education, which besides have undergone significant transformations since the Middle Ages. However, what exactly they should be is a question widely discussed in the Russian Orthodox environment. The article also analyzes the problem of perception of the theory of evolution in the Orthodox environment, which is still the most painful topic for Orthodox theology of science and Orthodox believers. The author also pays attention to some associations of Orthodox scholars in Russia, which differ significantly from each other.