The Mineral Collection of the Chamber of Commerce and Trades in 1866 comprised about 200 objects. Thanks to the concern of Antun Drobac (1810-1882) the number of items in the collection rose rapidly over the years. Dubrovnik men who were employed in the Institute of Geology in Cairo, the Russian Mining Institute, Antonio Bey Figari, director of the Cairo Museum and Antun Catullo gave Drobac new mineral specimens. Drobac’s private collections together with the collections of the Chamber were the basis for the founding of the Patriotic Museum. When the Museum was opened in 1873, more than 5000 minerals were exhibited on wooden specimen trays. From 1931 to 1979 because of the constant moves of the Museum and the Collection, the number of objects declined, and today there are only 585 specimens in 444 inventory numbers.

Since 2015 the documentation of the collection has been run in a computer database. In 2016 the Collection of Minerals and Rocks was entered into the Register of Cultural Properties of the Republic of Croatia, as number 6590.

The Fish Collection of Dubrovnik Natural History Museum has been put together ever since the founding of the museum in 1872. The periods in which the most additions were made were during the eras of Baldo Kosić, Milivoj Ulaga and Andrija Lesinger. Between 1882 and 1917 teacher, natural historian and taxidermist Baldo Kosić collected, determined and prepared an almost complete collection of fish of the Dubrovnik region. Unfortunately the wet part of the collection was destroyed during World War II, and part of the dermoplastic specimens deteriorated thanks to frequent moves, improper handling and inappropriate storage. After the death of Kosić, the Museum had no preparator until 1953, when Milivoj Ulaga arrived on the scene, and he, in collaboration with the Oceanographic Station – today the Marine and Coastal Institute, assembled a new collection of fish preserved wet and also made part of the still existing dermoplastic preparations. But after just a few years doing this job, Ulaga was transferred. Taxidermist Andrija Lesinger arrived in the Museum in 1960, and started on the lengthy process of restoring the old collection. He also collected new material and made about 170 preparations, which were on show until the earthquake of 1979 that closed the Museum. From 2011, new material has been collected.

The collection has been processed in its entirety, and the documentation has been kept in a computer database since 2013. Since 2015 it has been number 6590 in the Register of Cultural Properties of the Republic of Croatia.

Although the oldest preparation in the Collection of Birds derives from 1867, the first vigorous approach to collection came during the time of Baldo Kosić (1829-1918), who prepared an almost complete collection of birds from the Dubrovnik region. Over the years, as a result of the many moves the Museum had to endure, a part of Kosić’s collection deteriorated. When a new preparator, Andrija Lesinger, arrived in 1960, the length and sensitive procedure of salvaging the remains of Kosić’s collection of birds began. Lesinger also started collecting new scientific and exhibition collections made in the form of dioramas. The earthquake of 1979 considerably damaged the Museum’s building, which had to close. Not long after that, when the preparator went into retirement, the museum found itself without a professional staff.

To date about 1051 museum objects in the Bird Collection have been preserved. The collection has 246 species of birds from the fauna of Croatia. They are categorised into 18 orders, the most numerous of which is the Passeriformes, with 106 species and 528 specimens. Also well represented are the orders of the Charadriformes and the Falconiformes. Among the species in the Collection, 79 of them are on the Red List and 48 in the Red Book of Endangered Birds of Croatia. Among birds currently extinct in Croatia is the Pharaoh’s chicken, Neophron percnopterus, which nested in Croatia until the early 1980s, the great bustard, Otis tarda, which regularly overwintered in the Croatian coastal region at the turn of the 19^th and 20^th century, as well as the black and white northern Atlantic auk, Alca torda, recorded for the last time in 1909. Among species that are particularly noteworthy for the Dubrovnik area the critically endangered Accipiter brevipes, Levant sparrow hawk, deserves particular mention, nesting in Croatia only in the Konavle area, and the white Tachymarptis  melba or Alpine swift, which is actually in Croatia most abundant in Dubrovnik.

The Mollusc Collection is one of the oldest in the Museum. It was created in the 19^th century, most of the credit for the establishment and assembling of it going to the founder of the Museum Antun Drobac. President of the Chamber of Commerce and Trades in Dubrovnik, he had been approached by Dubrovnik people all around the world about the idea of founding a technical school in the city. A precondition for such a school was that it should have technical and natural history practical rooms richly furnished with collections. Thus Drobac started an initiative for collecting various kinds of cultural and historical, ethnographic and other valuable objects, above all “naturalia”, but because of the refusal of the government in Vienna to grant permission, the original idea of a technical school was modified, and the idea of creating a museum took its place. The basis of the Museum was to consist of his own collections, among which was the Collection of Molluscs. Also to be credited with the assembly of the collection was his contemporary, Fra Ivan Evanđelist Kuzmić, who had gone deeply into a study of the bivalves and snails of southern Dalmatia. The collection was supplemented by Baldo Kosić with examples of molluscs from the Dubrovnik area, on the whole sea snails, bivalves and cephalopods. The great Croatian natural historian Spiridon Brusina also enriched the collection with donations; during his many years of work, he discovered a hundred or so new species and subspecies of recent snails and bivalves.

This collection came into being in the19th century, and by 1900 88 specimens had been collected and prepared. It was later supplemented with specimens from Africa and South American sent to the museum by emigrants. But few of the specimens have been preserved to this day, most impressive being the leatherback turtle, Dermochelys coriacea, the first one every noted in the Adriatic. It was taken in September 1894 off the islet of Sv. Nikola, near Budva in Montenegro. The then director of the Patriotic Museum, Baldo Kosić, prepared this example, a male 2.14 m long, weighing 500 kg. He also preserved the gullet and part of the skeleton, but unluckily during the shifting of the museum material over the years all traces of these objects were lost.

The Collection was started in the 19^th century; it consisted of preparations from Africa, Australia and South America, although most of the exhibits were actually from the surroundings of Dubrovnik, near or far. Today a lesser number of exhibits is in existence, of which the most noteworthy are the otter, Lutra lutra, caught in Zaton, the Mediterranean monk seal, Monachus monachus, taken in Molunt, and the right lower part of the jaw of a Balaenoptera musculus, blue whale, from the Bay of Bisvay.

The Collection of Algae of Dubrovnik Natural History Museum is a gathering of several private collections; the work of collecting even predates the founding of the Patriotic Museum. Matija Botteri collected algae along the coastline from Dubrovnik to Lošinj between 1865 and 1867. Maritime engineer Petro Vidojević, from 1878 to 1881, gathered algae along the shores from Korcula to Rijeka. His herbarium was donated to the Museum by his widow, Jenni, in February 1905, at the time Baldo Kosić was active, as shown by his register. Apart from that there are several specimens of algae collected by the first Croatian female botanist, Marija Selebam de Cattani (1789-1870).