Rayquaza is a large, green, serpentine creature. It has red-tipped, rudder-like wings on its shoulders and down its body, and similarly patterned fins on the tip of its tail. Yellow ring-like symbols run across the length of Rayquaza's body and it has an additional yellow ring on top of its head. Rayquaza has two limbs with three-clawed hands, and two long, flat, horn-like structures on its head, with two shorter horns along its jawline. It has small, yellow eyes with black pupils, prominent pink gums, and two discernible fangs in its upper jaw.
As Mega Rayquaza, its body becomes longer and gains more features. Its head becomes longer with the Δ symbol appearing on its forehead. Its eyes now contain yellow pupils and red irises, and black, tree-like markings trail behind its eyes. Its red lips and teeth become gold, and the gold lines connect to those on its lower horns, which take on a broad, triangular shape. At the outer edges of its lower horns are long, golden, glowing tendrils that each extend to a green, fin-like structure; these tendrils have ring patterns that strongly resemble the yellow markings running along the length of Rayquaza's normal form. Its two upper horns become longer with a gold line running over them in a V shape, and each upper horn has another glowing tendril that ends in a circular shape with a spike. Along the length of its body are golden, glowing orbs placed where its ring patterns used to be. The chin, part of the neck, and parts of its serpentine body are changed to the color black. The fins running along its body are now marked with gold lines; the fins on its tail become entirely yellow and substantially longer. Particles stream from the long tendrils that extend from its jutting jaw; these particles can control the density and humidity of the air, allowing Mega Rayquaza to manipulate the weather. Its green hide sparkles with an emerald-like quality.
Inside Rayquaza's body lies an organ that contains the same power as a Mega Stone. A Devon Corporation scientist named this organ the mikado organ (Japanese: ミカド器官). By consuming meteoroids as it flies through the stratosphere, the mikado organ will be filled with enough energy to enable Rayquaza's Mega Evolution.
It is able to soothe the other members of the weather trio, even in their Primal Forms. Rayquaza is said to have lived for hundreds of millions of years in the ozone layer, where it feeds on water and other particles. Rayquaza is rarely seen by people; even in flight, its appearance is indistinguishable from that of a meteor. Rayquaza is the only known Pokémon capable of learning the move Dragon Ascent.