The Palaeobotany Collection dates back to the original collections acquired by the Museum's first director, Sir Frederick McCoy. The collection contains more than 50,000 specimens of fossil plants, spanning over 400 million years of geological time from the Palaeozoic to Cenozoic. Impressions of leaves, stems and plant remains form the majority of the specimens, together with petrified wood and fossil seeds. These specimens range in size from microscopic (less than 1 mm) to large (more than 1 m), with most specimens in the 5-25 cm size range. The bulk of the collection comprises Victorian material, but there are also significant holdings of specimens from other states and overseas.
While the main focus of the collections is Australian, in particular Victorian material, the overseas collection is arguably the most comprehensive in Australia. The collection of Baragwanathia and related flora from Victorian localities in Silurian and Lower Devonian sediments is of particular importance as these specimens are amongst the world's oldest known vascular land plants. The collection documents the development of land plants and the changing flora over time through changing climatic conditions in Victoria. It is a vast resource for research projects linking the extinct and modern flora of Australia and for understanding palaeogeography (how landmasses were arranged in the past). The large collection of well-documented Mesozoic plants fossils is also important for correlations of oil and gas-bearing strata within the Otway and Strzelecki Basins and in international correlation studies.