The formation of library was started with the first days of observatory establishment. Archival materials show that in the mid-19th century, more than a half of the observatory annual budget was spent to purchase books and periodic publications. In 1871, the first library catalog was compiled by K. Knorre. It consisted of 2600 units of books, pamphlets and near 8,000 units of the fund. The worthy successor in the organization of library was the second director of the observatory - I. Kortatstsi. The fund was enlarge with valuable special literature in astronomy of that time.

In the early twentieth century, the Naval observatory became a Southern department of Pulkovo Observatory and the library was completely saved for the future use by astronomers.

The fund consists of long-term collection of journals, among them Astronomical Journal (1950-2006), The Observatory, Publications of the Astronomical Society of the Pacific, Astronomische Nachrichten (1823-1933) etc. There are such publications as the Marine Collection (1854-1903), Notes of Admiralty Department (1828 - 1844), Report of the Chief of the Hydrographic Department (1861 - 1885), Novorossiysk Calendar (1841 - 1867), Brockhaus and Efron Encyclopedic Dictionary etc. Among the oldest printed books and handwritten documents can be identified "Geometry" by Rene Descartes (1683, Amsterdam), stylized version of the old edition of New Astronomy by Johann Kepler (1929, Munich-Berlin), anniversary facsimile edition of the manuscript On the Revolutions of the Celestial Spheres by Nicolaus Copernicus (1972, London-Warsaw-Krakow). The collection of maps and atlases includes Bode's Celestial Atlas Uranographia (1801, Berlin), the Atlas of Black Sea by E.I. Manganari (1841, graved in St. Petersburg). Nowadays, the library fund includes about 70 000 printed units. Reference and search tool of the library is a system of directories and files that provides different kinds of search,such as systematic and alphabetical catalogs, filing domestic and foreign periodicals. Currently, an electronic catalog has been created.