Abstract: The urgency of this problem is caused by the emergence of global challenges in the form of secularization, radicalization and globalization, thereby defining the strategy for the development of Islamic education and its role as an integrated system in addressing the challenges of Russian Muslims community. The article aims to analyze the conceptual aspects of Islamic education development in Russia, namely within the boom of mosque construction, the formation of the Muslim communities and their organizational structures in the 1990-ies the problems are revealed which worry our society and which led to negative phenomena, such as fragmentation and unhealthy rivalry of muftiats, legal and administrative obstacles that impede constructive social and spiritual activities, which appear on the basis of foreign influence and radical and extremist ideas among the youth.