The Department of Palaeobotany collects and elaborates collections of 100,000 items, including fossil flora and contemporary plant specimens which serve as comparative material for researchers.

The fossil materials are divided into three subsets: flora older than Paleogene (older than 65 million years), flora of Paleogene and Neogene (65 million years - 2.6 million years) and Quaternary flora (2.6 million years to the modern time) containing numerous archaeobotanical materials collected from archaeological sites. The oldest flora is dominated by coalfield remains, mainly leaves, but also fragments of shoots, seeds and cones as well as spores and pollen grains. In the collection there are specimens in the form of fragments of rocks in which parts of plants are preserved as mineralized remains, mainly trunks or branches, cuticle and palynological slides. The collection of Paleogene and Neogene flora is rich in fruit and seeds as well as specimens in the form of rock fragments with impressions or coalfield remains, preparations of whole leaves and other fragments of plants and cuticles slides. Quaternary flora is composed mainly of fruits and seeds, but also leaves, fruit scales, cones and wood. Archaeobotanical material obtained from archaeological sites of different age is dominated by charred, uncharred and mineralized plant macroremains such as fruits and seeds, but there are also charcoals and plant impressions in ceramics and clay daub.

Comparative collections of modern plants have been systematically created since 1954. They consist of a carpological material of fruits and seeds, leaf herbarium, cuticular slides, woods and charcoals, peat units and peat-forming plants. Noteworthy is the unique palynological collection of about 20,000 microscopic preparations.

The collection located in the Department of Palaeobotany of W. Szafer Institute of Botany, Polish Academy of Sciences in Cracow is the only one of its kind in Poland and one of the few in Europe and serves as a base for studies and various research works for students and scientists.

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