Zekrom is a black, bipedal Pokémon resembling a dragon or dinosaur, with dark patches on various portions of its body. It has red sclerae, white irises, and black pupils, as well as a small horn-like protrusion on the tip of its snout. Its head sports a thundercloud-like crest tipped with light-blue coloration. There are six pairs of pointed teeth visible when its mouth is open, two in the upper jaw and four in the lower. At the base of its neck is a black, stud-like feature, and atop its shoulders are similar, larger features resembling armor padding. The bases of its wings also have such padding, and a fanned, splayed, seemingly webbed shape with a small "wing-spike" on one edge. The lower length of Zekrom's arms extenuate into splayed, seemingly webbed, somewhat baseball-mitt-like formations, with three-clawed, dark-colored hands on the undersides. The front portion of Zekrom's waist is black-colored, with its belly and thighs having thin striations down their length. Its knees are black, as are the foremost parts of its three-clawed feet and spiked heels. When its emotions surge, it enters Overdrive mode and its tail lights up with a blue light.
Zekrom's tail consists of large, round, conical and spiked formation, likened to an electricity generator, with a black inner portion and bands on the tip of the outside portion. This tail produces energy for its attacks and emits an anti-gravity field, allowing Zekrom to fly through the air with minimal effects from aerodynamic resistance and gravity. It can cause several thunderstorms in one area, and it normally hides in thunderclouds. In an Unovan myth about the twin heroes, Zekrom sided with the younger brother who sought ideals. According to one myth, Zekrom uses its lightning to annihilate kingdoms of people who have lost the righteousness in their hearts.