1539 in science
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- Hieronymus Bock publishes the first edition of his flora of Germany, the Kreutterbuch, adopting a new system of classification based on his observations.
- May 30 – Hernando de Soto lands at Tampa Bay, Florida.
- August–September – Francisco de Ulloa explores the Gulf of California.
- Johannes Baptista Montanus is appointed professor of medicine at the University of Padua where he introduces clinical medicine, including bedside examination, into the curriculum, integrating theory and practice.
- September/October – José de Acosta, naturalist (died 1600)
- exact date unknown – Olivier de Serres, soil scientist (died 1619)
- August – Vannoccio Biringuccio, Italian metallurgist (born 1480)