All coffee beans come from plants in the genus Coffea. Although there are thousands of species of plants within this genus, with tremendous variance in size and shape, only two are of commercial importance: Coffea arabica, and Coffea canephora, the latter more commonly called robusta, after a prime variety. A third species, Coffea liberica has found some localized production in Liberia, but it is of minor significance in the global market.

Arabica is genetically distinct: it has four sets of chromosomes, whereas robusta, and liberica each have two.

Coffee beans are the seeds of the coffee "cherry"; two seeds normally grow within each cherry. On the tree, the beans are covered by the silverskin (a vestigial remainder of the fruit's development, also called the spermoderm). The silverskin is covered by a parchment skin (the endocarp), which is covered by a slimy layer (the parenchyma), surrounded by a thin layer of pulp (the mesocarp), all covered by an outer skin (the exocarp). These layers must be removed prior to roasting, though some silverskin often remains attached.