The Micropalaeontology Collection contains over 40,000 microscope slides and residues containing microfossils. The collection mainly consists of slides containing fossil pollen along with residues from drill core samples that contain foraminifera and other microfossils from the Gippsland and Otway Basins. This material has been collected during exploration and development of oil fields in Bass Strait. The bulk of the Micropalaeontology Collections has come to the Museum since 1975, when a legislated agreement, originally with the Department of Mines and now managed by the Department of Environment, Land, Water & Planning, stipulated that the Museum would be the legal repository for all studied slides and residues from oil exploration in Victoria.
The collection of Gippsland and Otway Basin micropalaeontology specimens is of high economic significance as it enables detailed and precise sequencing of the Victorian oilfields. This makes them particularly important to the Oil Industry. The collection is also invaluable to researchers in reconstructing past terrestrial environments and climates by using pollen to identify species that would have been present.