Gemstones are identified by Gemologists, who describe gems and their characteristics using technical terminology specific to the field of gemology. The first characteristic a gemologist uses to identify a gemstone is its chemical composition. Diamonds, for example, are made of carbon (C) and rubies of aluminium oxide (Al2O3). Next, many gems are crystals which are classified by their crystal system such as cubic or trigonal or monoclinic. Another term used is habit, the form the gem is usually found in. For example diamonds, which have a cubic crystal system, are often found as octahedrons.

Gems are classified into different groups, species, and varieties. For example, ruby is the red variety of the species corundum, while any other color of corundum is considered sapphire. Emerald (green), aquamarine (blue), bixbite (red), goshenite (colorless), heliodor (yellow), and morganite (pink) are all varieties of the mineral species beryl.

Gems are characterized in terms of refractive index, dispersion, specific gravity, hardness, cleavage, fracture, and lustre. They may exhibit pleochroism or double refraction. They may have luminescence and a distinctive absorption spectrum.

Material or flaws within a stone may be present as inclusions. The gem may occur in certain locations, called the "occurrence."