Using a light microscope chromoplasts can be differentiated and are classified into four main types. The first type is composed of proteic stroma with granules. The second is composed of protein crystals and amorphous pigment granules. The third type is composed of protein and pigment crystals. The fourth type is a chromoplast which only contains crystals. An electron microscope reveals even more, allowing for the identification of substructures such as globules, crystals, membranes, fibrils and tubules. The substructures found in chromoplasts are not found in the mature plastid that it divided from.
The presence, frequency and identification of substructures using an electron microscope has led to further classification, dividing chromoplasts into five main categories: Globular chromoplasts, crystalline chromoplasts, fibrillar chromoplasts, tubular chromoplasts and membranous chromoplasts. It has also been found that different types of chromoplasts can coexist in the same organ. Some examples of plants in the various categories include mangos, which have globular chromoplasts, and carrots which have crystalline chromoplasts.
Although some chromoplasts are easily categorized, others have characteristics from multiple categories that make them hard to place. Tomatoes accumulate carotenoids, mainly lycopene crystalloids in membrane-shaped structures, which could place them in either the crystalline or membranous category