The shooting has led to protests across the United States and spurred a debate about race and the laws of self-defence all the way to the White House and a comment from President Barack Obama: "If I had a son, he would look like Trayvon."
Special prosecutor Angela Corey announced the charges against the 28-year-old Zimmerman at a news conference on Wednesday.
"I can tell you, we did not come to this decision lightly," she said after a weeks-long investigation into the death of 17-year-old Martin on February 26.
Corey said Zimmerman turned himself in to authorities, who then arrested him and transferred him to a county jail in Sanford, Florida.
He had gone into hiding shortly after the shooting and telling police he shot Martin in self-defence. He was not charged at that stage as police said they found no evidence to contradict his account.
A new lawyer for Zimmerman said his client will plead not guilty. Mark O'Mara said people should not jump to conclusions about his client's guilt. He says he's "hoping that the community will calm down" now that charges have been filed and the case is moving forward.
Prior to the announcement of the charges, Martin's mother Sybrina Fulton said she knows "justice will be served" in her son's death.
The Martin family and their lawyer Benjamin Crump had earlier renewed their pleas for calm.
Crump said the family wants communities nationwide to remain calm in response to the prosecutor's decision.
"We don't need anybody taking these matters into their own hands," Crump said.
Fulton and Trayvon's father Tracy Martin spoke at a news conference in Washington, where Attorney General Eric Holder said earlier that he would take appropriate action if evidence of a civil rights crime is found in the shooting.
'Emotionally crippled'
Zimmerman has been so "emotionally crippled" by the racially charged case that he may no longer be in control of his actions, his frirst set of lawyers said on Tuesday.
Lawyers Craig Sonner and Hal Uhrig said they had not heard from Zimmerman since Sunday and that they could no longer claim to act as his legal representatives, since he had failed to take their phone calls or respond to emails and had taken several recent actions without their advice.
Among other actions, they said Zimmerman had taken the unusual step of trying to personally contact Corey, the special prosecutor who is handling his case.
"George Zimmerman, in our opinion and from information made available to us, is not doing well emotionally," Uhrig said.
Uhrig and Sonner spoke at a news conference outside the Seminole County Courthouse in Sanford, Florida, the town where Martin was killed.
Both lawyers said they had never met face-to-face with Zimmerman, but had been in regular contact with him before Sunday.
"He's gone on his own," Sonner said of Zimmerman. "I'm not sure what he's doing and who he's talking to."
He did not elaborate on the suggestion that Zimmerman had somehow gone rogue, after contacting a high-profile TV journalist and starting up a website to raise money for his legal defence.
Corey, the special prosecutor, said in a statement that she would hold a news conference sometime later this week to discuss "new information" about the case, but said nothing about Zimmerman's whereabouts or emotional state.
Uhrig and Sonner said Zimmerman's attempt to phone Corey and speak to her directly on Tuesday was rejected out of hand by her office because he did so without legal counsel.
Police cited Florida's "Stand Your Ground" law, which allows people to use deadly force against adversaries when they fear great bodily harm or death.
