For bosses please see Super Metroid/Bosses.
Electrical beings resembling the nucleus of an atom. They sometimes emerge from glass-encased storage tubes attached to the floor of the Wrecked Ship.
A round, floating creature, which emits puffs of gas from many exhaust pipes on its surface. It is attracted to Samus and moves toward her, but can only be destroyed with a Super Missile or the Grappling Beam. They can be found in the Wrecked Ship and the sand pits of Maridia.
The cacatac is a plant standing roughly 1.3 meters in height, and is found in Brinstar, Norfair, and Maridia. It stands on a number of short spiney legs. The cacatac's body is covered by rows of spikes, which it is able to launch as projectiles. Though normally green, cacatacs can be and are found in a variety of colors, including red and blue.
Covern (sometimes called Koben) are ghosts that haunt the Wrecked Ship in Super Metroid. They are dark brown and have multiple skull-like heads. After the defeat of Phantoon, they will cease to haunt the ruins, suggesting that they were in fact caused by Phantoon. They try to materialize wherever Samus Aran is standing, but the player can simply move and then shoot them to kill them.
The KiHunters are insectoids closely resembling wasps or praying mantises. They have four limbs and a set of wings. They are most common in their flying form, where they attack with their claws by swooping down upon their victim from above. All members of the species will lose their wings when damaged. They then revert to a ground-based mode of travel that involves hopping, and at this point they will spit highly corrosive acid at anything that threatens them.
Jellyfish like creatures that latch their mandibles onto pray and suck out their life for food. Metroids have appeared in every Metroid game, in various forms. They appear in different sizes and forms, but the most common are the original jellyfish-like ones.
In Super Metroid, all metroids except one (in a previous encounter, Samus "befriends" a baby metroid and eventually sets it free) are enemies of Samus. The baby metroid that Samus once found has also made its way to Planet Zebes and is now a full grown adult. It aids Samus in her fight with the final boss of the game.
Creatures similar to metroids that can't latch onto prey. They drain the energy of their prey just like normal metroids. The mochtroids can be found in Maridia.
A green mollusk which can curl up into a ball much like Arachnus to block passages. They are only found in a single area in Maridia.
 Shriek Bats/Skrees
Shriekbats are bat-like aerial creatures who hang upside-down from ceilings. They have an extremely high body temperature and are very territorial - if anything wanders into their territory they fly towards the intruder and dig through the ground. They have two large claws, and when they slam into the ground they scatter debris from drilling into the ground (traveling only a few spaces from point of impact).
The hopping enemies from the original Metroid are back, and are faster than ever. These guys attack by hopping around, hoping to land on you with crushing force.
 Space Pirates
Space pirates are the first units you encounter within Super Metroid. They look like mechanical praying mantes with serrated arms. They have the ability to shoot lasers and leap from wall to wall in small areas.
 Gray Pirates
Use your power beam (standard)
 Green Pirates
Regular Missiles work on these baddies
 Red Pirates
Rare and found in Norfair, use the speed booster
 Pink Pirates
Cannot be killed unless the plasma beam is obtained. However, they can be killed with the speed booster
 Gold Pirates
Only the screw attack can kill them (not the pseudo screw attack)
 Tan-Gray Pirates
Commonly dubbed 'ninja pirates,' they are the most powerful Space Pirate in Super Metroid and are found only in a room near Ridley's where they function as a miniboss of sorts. They have such powerful armor, they can only be destroyed by charged shots and super missiles, and only once they turn gold (which occurs after they do a spin-jump). Rather than firing lasers like other space pirates, they rely on spinning jumps, a few karate moves, and flying kicks. They also occasionally throw their claws (resembling boomerangs when airborne), which somehow respawn a short time later.
 Red Zoomer
Alternatively, a red version exists; labelled an easter egg for it's strange behavior and how it does not affect gameplay at all.
There is a common mixup between Zoomers and Geemers, in that Geemers are the upgaded version of Zoomers (in Metroid Prime Geemers have retractable spines) with a higher tolerance to firepower.
Yellow organisms very similar to crabs. They behave exactly like Geemers, but exist in water. They inflict more damage and have more health than Geemers.