The library collects literature on botany and related to it fields - bryology, ecology, phycology, lichenology, palaeobotany, floristics, geography of vascular plants, dendrology, mycology, nature conservation, environmental protection, forestry, agriculture, horticulture, soil science, geology, archeology, geography, chemistry, physics, medicine and others.

Apart from the specialized magazines and textbooks, there are also collections of maps, slides, microfiches, botanical atlases, dictionaries, natural science and geographical lexicons  and encyclopedias, language dictionaries, as well as collections of a popular science literature.

At the end of 1997, the Library had 163,510 volumes, including 121,635 books and booklets, 34.835 volumes of journals, 7,040 maps, microforms and slides.

In addition to the basic collections of books, journals, and booklets, the Library also has 736 old prints. The old prints have been collected by botanists and bibliophiles from the Kraków Region, mainly Józef Rostafiński, Władysław Szafer, and Jadwiga Dyakowska. Among the oldest printed natural history books, or herbaria, the Library's collection includes:

Dorstenius Theodoricus – Botanicon continens herbarum aliorumque simplicium. Frankfurt, 1540 (the oldest book of the collection).

Lonicer Adam – Vollständiges Kräuter-Buch oder das Buch über Reiche der Natur. Augsburg, 1793.

Du Pinet – Historia Plantarum ex Dioscorici. Lughduni, 1561.

Siennik Marcin – Herbarz, to jest ziół tutecznych, postronnych i zamorskich opisanie. Kraków, 1568.

Syreniusz Szymon – Zielnik. Cracoviae, 1613.

Unique for Poland is the collection of old flora, containing many rare works, such as the first flora of the Tatra Mountains by G. Wahlenberg, Flora Carpatorum Principalium exhibens plantas in Montibus Carpaticus inter flumina Waagum et Dunajetz (Göttingen, 1814). The illustrated atlases of flora are notable because they are masterpieces of the printing art, e.g. Schmidel D. Casimirus Christophorus' Icones plantarum et analyses partium aeri incisae atque vivis coloribus (Erlangae, 1793).

Botanical Polish editions (Polonica 259 items) contain classical works of Polish botany of the 18th century, such as those by Krzysztof Kluk, Stanisław Bonifacy Jundziłł, Gabriel Raczyński and many others. Among the rarities are also old botanical textbooks, dating from the period of Carolus Linnaeus to the authors of the 19th century (Edward Strassburger, Józef Rostafiński), to the textbooks published in the first half of the 20th century (e.g. by Richard Wettstein, Dezydery Szymkiewicz, Emil Godlewski, and others).