The First Russia-wide Congress of Naturalists and Doctors held in the Assembly Hall of Saint Petersburg Imperial University in December 1867 – January 1868 recognized a pressing task to educate learned societies in natural science. It was the idea of a chairman, famous zoologist, principal of Saint Petersburg University in 1867-1873 and professor Karl Fedorovich Kessler to form the societies under all Russian universities which would have become an important precondition for nature research in all regions of Russia. Basically, it was a far-sighted and ingenious idea to found a network of institutions particularly focused on environmental assets research in Russia without engaging in additional human resources.

The permission of His Imperial Majesty Emperor Alexander II to form such societies was obtained in February 1868. After that Russian Chemical Society (nowadays Mendeleev Centre) and Society of Naturalists were founded under Saint Petersburg University. In 1869, Societies of Naturalists were opened under Universities in Kiev, Kazan, Novorossiysk and Kharkov. Similar institutions appeared afterwards in Derpt University (1887), University of Warsaw (1888) and Tomsk University (1889). The process of learned bodies forming continued with Ekaterinoslav Scientific Society foundation in 1901 and Crimean Society of Naturalists and Nature Lovers - in 1910.

The main goals of Saint Petersburg Imperial Society of Naturalists, which were established in the first Statute of the society in 1868, were to assist Russian nature research, promote natural science, carry out the spread of knowledge in natural science and facilitate communication between Russian scientists. At the present day, top-priority goals of the Society are complex research in natural science where its various disciplines overlap, wildlife preservation mainly in the Northwest Region of Russia; support of communication between naturalists of Saint Petersburg and Russia; junior naturalists assistance.

In order to reach the objectives established in the Statute, the Society puts into practice number of activities: public plenary meetings, conferences, publishing activities, the international "Kowalevsky medal" award, research papers competition for SPbSN members, competition of master's and graduation theses, provision of scholarships to biology and geology students of Saint Petersburg higher education institutions.

Present-day structure of the Society reflects both its history and the recent evolution. Historically SPbSN consisted of "Botany", "Zoology and Physiology" and "Geology and Mineralogy" sections. Subsequently network of sections was formed, which represents increasing differentiation of natural science and advent of cross-disciplinary areas of activity (currently the number of sections and subdivisions that function as sections exceeds 20).

General Meeting is a supreme governing body of the Society, held not less than once in five years. Scientific Council headed by the President of the Society supervises activities of the Society between the General Meetings.