A naturally small tree, Jonathan is roundish or spreading in form and somewhat droopy. It is self-fertile but, as ever, better crops will be had in the presence of a pollenizer. Jonathan is susceptible to all major apple diseases, but only moderately, and it is not considered a remarkably difficult tree to cultivate. It is considered to be resistant to brown rot. Jonathan should be thinned carefully to avoid biennialism.

The apple is medium sized, round, and red flushed over a greenish yellow background. There is usually a small amount of russeting around the stem. The flesh is firm, snappy, and juicy, and the flavor is refreshing, full, and balanced. In Apples of Uncommon Character, Rowan Jacobsen describes Jonathan as "the essence of the American apple ... spicy, uncomplicated, sweet-tart." This is a lovely tree to plant for children.

It is widely agreed that Jonathan is a seedling of Esopus Spitzenberg. It first grew on the farm of Philip Rick in Ulster County, NY in the 1790s, but it was not until a Mr. Jonathan Hasbrouck introduced the apple to his friend Judge Jesse Buel in 1826 that the tree received any real attention. Judge Buel happened to be president of the Albany Horticultural Society, and he both named the apple after his friend and began disseminating scion wood. Jonathan has been widely used in breeding programs; its illustrious offspring include Idared, Melrose, Jonagold, Jonafree, Jonamac, and Akane.