The Light - The primary antagonists of the Season 1 who plotted and engineered various events throughout the series. The group was conceived by Vandal Savage who isn't the leader, but rather the first among equals.[52] The identities of the leaders are known only to a very select group of individuals that work with them.[53]

Vandal Savage (voiced by Miguel Ferrer) - Member of the Light under the designation of L-1. As mentioned above, he isn't the leader, but had conceived the group.

Ra's al Ghul (voiced by Oded Fehr) - Member of the Light under the designation of L-2 and leader of the League of Shadows.

Lex Luthor (voiced by Mark Rolston) - Member of the Light under the designation of L-3 and CEO of LexCorp. He played a part in the creation of Superboy by donating his DNA.

Queen Bee (voiced by Marina Sirtis) - Member of the Light under the designation of L-4 and dictator of Bialya.

• Psimon (voiced by Alan Tudyk) - The right hand of Queen Bee who has telepathic powers. He often faces Miss Martian in telepathic battle, and was once put into a catatonic state by her.

Ocean Master (voiced by Roger Craig Smith) - Member of the Light under the designation of L-5 and the half-brother of Aquaman. Sometime after the events of Season 1, he was somehow disgraced and was replaced with Black Manta.

Brain (voiced by Nolan North in the first unofficial appearance, Corey Burton in the first official appearance) - Member of the Light under the designation of L-6.

• Monsieur Mallah (vocal effects provided by Dee Bradley Baker) - Brain's gorilla sidekick.

Klarion the Witch Boy (voiced by Thom Adcox-Hernandez) - Member of the Light under the designation of L-7. According to Greg Weisman, Klarion joined the Light mostly because it seemed like fun.[54]

Black Manta (voiced by Khary Payton) - An associate of the Light and Aqualad's father. In Season 2, Black Manta has replaced Ocean Master on the Light.

The Injustice League - A small group of villains who used plant-like creatures to attack the Earth in "Revelation." They seemed to play as the masterminds behind events in Season 1, but in reality they were scapegoats to distract the Justice League from uncovering the true masterminds: the Light.

Atomic Skull - A S.T.A.R. Labs scientist turned supervillain and enemy of Superman.

Black Adam - The main antagonist of Captain Marvel.

Count Vertigo (voiced by Steven Blum) - Member of the royal family of Vlatvia obsessed with seizing power from his niece Queen Perdita.

Joker (voiced by Brent Spiner) - The main antagonist of Batman.

Poison Ivy (voiced by Alyssa Milano) - A plant manipulator and enemy of Batman.

Ultra-Humanite (vocal effects provided by Dee Bradley Baker) - Supervillan primate with super-human strength and intellect and enemy of Superman.

Wotan (voiced by Bruce Greenwood) - Immortal sorcerer and main antagonist of Doctor Fate.

Blockbuster / Mark Desmond (voiced by René Auberjonois) - Mark Desmond is a scientist who works at Project Cadmus and works for the Light. He created the Blockbuster formula and helped Lex Luthor to create Superboy. When Robin, Aqualad, Kid Flash, and Superboy were about to escape the Cadmus building, Mark Desmond ingested the Blockbuster formula becoming Blockbuster.

T. O. Morrow (voiced by Jeff Bennett) - The scientist responsible for creating Red Tornado and an operative of the Light. He also created Red Torpedo and Red Inferno to infiltrate the Justice Society of America, both of which failed. He worked with Bromwell Stikk to test out the Mister Twister armor. It is later revealed that T.O. Morrow was in a coma and that he built an android in his place.

Professor Ivo (voiced by Peter MacNicol) - A mad scientist and associate of the Light. He was the one who created Amazo and helped Brain and Klarion the Witch Boy weaponize the Starro-Tech.

Sportsmaster (voiced by Nick Chinlund) - A sports-themed agent of the Light. He is the ex-husband of Paula Crock and the father of Artemis and Cheshire.

League of Shadows - A group of assassins that are led by Ra's al Ghul and carry out the bidding of the Light.

Black Spider (voiced by Josh Keaton) - A spider-themed assassin.

Hook - An assassin with a hook for a hand.

Professor Ojo (voiced by Nolan North) - A scientist who wears a special helmet to see.

Sensei (voiced by Keone Young) - A high-ranking member of the League of Shadows.

Cheshire (voiced by Kelly Hu) - Member of the League of Shadows, the sister of Artemis, and the daughter of Sportsmaster and the Huntress. In Season 2, Cheshire is shown to be married to Red Arrow with whom they have a child and has left the services of the League of Shadows. She informs Red Arrow on where the real Roy Harper is located, and together they rescue him.

Hugo Strange (voiced by Adrian Pasdar) - Warden of supervillain prison Belle Reve who is also an operative of the Light. He is responsible for Professor Ivo's temporary breakout on behalf of the Light so that Professor Ivo can weaponize the Light's Starro-Tech.

Riddler (voiced by Dave Franco) - An enemy of Batman who specializes in riddles. He was an inmate at Belle Reve and the only one to escape during Icicle Sr.'s failed breakout attempt. Riddler is also shown to be an agent of the Light as he was seen helping Sportsmaster secure a part of Starro from S.T.A.R. Labs.

Kroloteans - An alien race that are recurring enemies in Season Two. One Krolotean used a special suit to masquerade as General Tseng only to be exposed and taken away by Lobo. Another one tried to masquerade as Bibbo Bibbowski only to be stopped by Blue Beetle, Bumblebee, and the real Bibbo.

The Partner (voiced by Kevin Grevioux) - An as-yet-unidentified partner of the Light who has only been seen in silhouette and is feared by the Kroloteans.

Superboy, alias Conner Kent, is a clone of Superman in the Young Justice television series. He first appears in the premiere episode "Independence Day," but late in the episode, as an experiment conducted by Project Cadmus. He was engineered to replace Superman in the event of the hero falling or otherwise becoming compromised. He was being psychically "educated," and when he decided to join the "sidekicks" of Justice League heroes Aquaman (Aqualad), Batman (Robin), and The Flash (Kid Flash), he attempted to form a connection with Superman, but the hero was initially reluctant to acknowledge Superboy.

As of the second season, Young Justice: Invasion, Superboy and Superman now get along, following a five-year gap between the first and second seasons. The reasonings behind their changed relationship have not been shown as of August 2012.