Jan became a professor of botany when many plants were imported from the Cape and Ceylon and a new system had to be developed.
Commelin amassed a fortune by selling herbs and drugs to apothecaries and hospitals in Amsterdam and other Dutch cities.
He also prepared for publication "Horti Medici Amstelodamensis Rariorum" which appeared in 1697 and dealt mainly with plants from the East and West Indies, and was illustrated mainly by Jan Moninckx and his daughter Maria Moninckx.
His nephew Caspar Commelin (1667-1734) became the director of the Amsterdam botanic garden after Peter Hotton left.
Caspar finished the work of his uncle and had it published with the help of Frederik Ruysch.