[4] Batsch discovered almost 200 new species of mushrooms, including Clitocybe nebularis, Calocera cornea, Paxillus involutus, and Tapinella atrotomentosa.

He was a recognised authority writing two books on the topic, Elenchus Fungorum (Discussion of Fungi, between 1783 and 1789), which is still highly rated today[5] and Versuch einer Anleitung zur Kenntniss und Geschichte der Pflanzen (Attempt at Instruction in the Knowledge and History of Plants, between 1787 and 1788).

Rejecting the system of Carl Linnaeus, he began to classify plants on the basis of their external form and shape and to make them generally understandable by means of a clear, precise representation, as best known in his three volume Elenchus Fungorum.While well versed in the flora of the Jena area, the weakness of his system lay in his lesser familiarity with the plants of the rest of the world.

[2] Other works include Dispositio Generum Plantarum Jenensium Secundum Linnaeum et Familias Naturales, Jena 1786, generally referenced as Dispos.

[6] His taxonomic classification of plants is summarised in his last work, the Tabula affinitatum regni vegetabilis (1802),[7] which was notable for its diagram depicting the network of affinities within the vegetable kingdom.