The article discusses the issue of the presentation of the history of science in the anti-religious expositions of the Leningrad museums of the 1920s – 1950s. During this period, the history of the development of science was viewed as the history of the struggle of scientific knowledge with ignorance and religious superstition, and natural science education was considered an integral part of anti-religious propaganda. Since 1930, after the First All-Russian Museum Congress, order has been introduced into the structure of anti-religious expositions. The practice of creating departments “Science and Religion” arises, in which materials were presented that propagandize the scientific picture of the world, illuminating the foundations of astronomical knowledge, the origin of life and human being. The report highlights the basic principles of constructing the “Science and Religion” departments of the State Anti-Religious Museum of the Leningrad Branch of the Union of Militant Atheists (1930-1941) and the Museum of the History of Religion and Atheism of the USSR Academy of Sciences (1954-1969). The two museums reflected different approaches to the presentation of religion. MHR, created in the system of the Academy of Sciences, in contrast to LSAM, subordinated to the system of political education and focused on solving propaganda problems, positioned itself as a research institution. However, in 1954 a special department was created there, the purpose of which was to show the radical opposition between science and religion and the role of Soviet science in overcoming religious superstitions.