The museum was first housed in the Villetta Di Negro, which had already belonged to the Marquis Gian Carlo Di Negro, located in the city centre and known to the Genoese as a meeting place for writers and poets. The Municipality acquired it and entrusted Doria with the task of turning it into the site for a museum. Initially, the exhibits consisted of the valuable zoological collections donated by Doria himself, including the specimens he had found during his travels to Persia (1863) and the island of Borneo (1865 together with botanist Odoardo Beccari), and two important collections inherited by the Municipality: namely, the geological and paleontological collection of the Marquis Lorenzo Pareto and the malacological one of Prince Oddone of Savoy. The subsequent growth of the collections, especially the zoological, was the result of the many explorations promoted by Doria, under the auspices of the Società Geografica Italiana, of which he was the president for many years. A number of distinguished scholars (who often became the authors of the description of these new species) took part in these trips to the Indo-Malay Archipelago, various regions of Asia, Africa and South America. Among others, Luigi Maria D’Albertis, Leonardo Fea, Arturo Issel, Orazio Antinori, and Odoardo Beccari

Given the increasing number of exhibits, the narrow Villetta Di Negro was no longer large enough to house the museum, which led to the construction of new premises, also thanks to the reputation gained by the Museum. The project was entrusted to architect Cordoni, who visited the major European museums with Raffaello Gestro before starting the works

The inauguration of the present museum takes place on 17 October 1912, at the annual meeting of the Society for the Advancement of Science. The ceremony is attended by scholars from around the world, except Giacomo Doria, whose disease had long brought him to immobility in his villa of Borzoli, up to his death on 19 September 1913. In the public session of 25 November 1913, the City Council approved the proposal to give the museum the name of its founder and to display a bust in his memory.

On the death of Doria, Raffaello Gestro, collaborator and researcher at the Museum since its foundation, was appointed director, remaining in office until 1934 and ultimately leaving a significant imprint with his work. After him, the subsequent directors were: Oscar de Beaux, mammalogist (until 1947) ; Carlo Alzona, malacologist (up to 1955) ; Enrico Tortona, ichthyologist and marine biologist (until 1976) ; Lilia Capocaccia Orsini, herpetologist (until 1996) ; Roberto Poggi, entomologist (until 2011) ; Giuliano Doria, herpetologist, from 2011 to present day.