Snake
Snake is a world-renowned soldier and infiltrator. Formerly affiliated with the CIA's FOX unit, Snake is now a mercenary commander with a following of fanatically-loyal soldiers organized into the unit Militaires Sans Frontieres (MSF). In the 1960s, he was sent into Soviet territory to assassinate his mentor The Boss, averting global thermonuclear war. After the completion of this "Operation Snake Eater" and saving the world, Snake became known among soldiers and mercenaries in the West and East as "Big Boss."
Kazuhira Miller
"Kaz" is Snake's best friend and right-hand man. Whereas Snake presents MSF with a vision, Kaz minds the details toward making that vision happen. Like almost all MSF soldiers, Kaz met Snake on the battlefield as his enemy but was drawn to the ever-growing legend of Big Boss. Kaz is friendly, flirtatious, well-read, and has a brilliant mind for business. His capabilities will help grow MSF into a force to change the world. He seems to be the one Snake trusts with mission control, offering Snake advice and command over the radio while Snake is in the field.
Paz Ortega Andrade
A girl from Costa Rica with a vision for world peace so strong, she besought Big Boss himself to help return peace to her country. She traveled to Columbia with Professor Gálvez to convince Snake and Kaz to deploy MSF to Costa Rica, telling them the story of her escape from the clutches of an unknown and illegally armed group. After this meeting, Paz remains in touch with Snake, offering him advice and information on Costa Rica's history and wildlife.
Amanda Valenciano Libre
Amanda is the eldest child of the Sandinista Comandante. She is fierce and fearless and a natural leader, inspiring her men and her kid brother Chico to continue to fight la revolución through the harshest most austere conditions. She becomes an ally of Snake, offering him tactical advice. When circumstances force her to take command of the Sandinistas, she struggles with feelings of inadequacy toward living up to the example of her father.
Chico
Ricardo "Chico" Valenciano Libre is the youngest child of the Sandinista Comandante and a child soldier. He frequently clashes with his elder sister Amanda over his right to prosecute la revolución despite being only twelve years old. Their fights frequently drive him to run away. His need to explore makes him ideally suited for intelligence and scouting. He has a child's fascination with strange wildlife, offering Snake a wealth of information about what the game calls "UMAs" (a Japanese term for cryptids).
Cécile Cosima Caminades
A birder from Paris who came to Costa Rica to observe the resplendent quetzal in its natural habitat, Cécile found herself captured and imprisoned by Dr. Strangelove for getting too close to the latter's laboratory. She was the one who recorded the voice of The Boss, which ultimately spurred Snake into accepting Paz's and Gálvez's mission. As an expert in ornithology, Cécile's knowledge will become instrumental in solving a puzzle during one of the game's missions. To a Japanese speaker, the phonetics of her full name sound like the words that translate into the phrase "Kojima is God."
Huey Emmerich
A roboticist in the employ of Hot Coldman and the Peace Walker project. Unable to walk himself, he is fascinated with the mechanics of bipedal motion and applied those mechanics to an unknown new weapon in development in Costa Rica. However, his motives seem pure; he's more interested in creating a nuclear deterrent that would rule out human error. He develops severe misgivings when he learns of Coldman's plans with Peace Walker.
Dr. Strangelove
An AI scientist in the employ of Hot Coldman and the Peace Walker project. She is responsible for the creation of the electronic brains that control of the unmanned weapons Chrysalis, Pupa, Cocoon, and Peace Walker itself. She is also interested in the capture of Snake to further her wish to understand The Boss's will. She is more interested in the potential of electronic minds rather than the potential of mankind.
Hot Coldman
Coldman is the CIA Station Chief in Latin America, shunted there from Langley after a falling out with the DCI. He personally oversees the development of the Peace Walker Project in a laboratory in Costa Rica. He is responsible for the operations of the armed group, the Peace Sentinel, in Costa Rica. He believes nuclear deterrence is based on the flawed logic that human beings would not necessarily retaliate against a nuclear strike and will go to any length to prove his theory. By all appearances, Coldman is the story's antagonist.
Ramón Gálvez Mena
Paz's benefactor who lectures at the University of Peace in Costa Rica. In reality, he is a KGB agent backing the FSLN rebels in Nicaragua and his plans involve Snake and MSF in some way. He goads Snake into accepting his mission with a recording of the voice of The Boss.
The Boss
The Boss was Snake's mentor and most beloved. She was known among soldiers all over the world as the "Mother of Special Forces." She and her supernatural team of soldiers known as the Cobra Unit led the Allies to victory in World War II. Her defection to the Soviet Union forced the CIA to send Snake to assassinate her in order to avert global thermonuclear war. Despite being dead for a decade, The Boss casts an immense shadow over the characters and events of this game.