George Zimmerman, 28, could get up to life in prison if convicted in the slaying of the unarmed black teenager.
Special prosecutor Angela Corey announced the charges but would not discuss how she arrived at them or disclose other details of her investigation, saying: "That's why we try cases in court."
Second-degree murder is typically brought in cases when there is a fight or other confrontation that results in death but does not involve a premeditated plan to kill. It carries a mandatory minimum of 25 years behind bars when a gun is used.
Martin's parents expressed relief over the decision to prosecute their son's killer.
"The question I would really like to ask him is, if he could look into Trayvon's eyes and see how innocent he was, would he have then pulled the trigger? Or would he have just let him go on home?" said his father, Tracy Martin.
Corey would not disclose Zimmerman's whereabouts for his safety but said that he will be in court within 24 hours, at which point he can request bail. He turned himself in in Florida.
Zimmerman's new attorney, Mark O'Mara, said: "I'm expecting a lot of work and hopefully justice in the end." On Tuesday, Zimmerman's former lawyers portrayed him as erratic and in precarious mental condition. But O'Mara said Zimmerman was OK: "I'm not concerned about his mental well-being."
Zimmerman, whose father is white and whose mother is Hispanic, has asserted since the Feb. 26 killing in Sanford that he shot in self-defense after the teenager attacked him. Martin's family argued Zimmerman was the aggressor.
The shooting brought demands from black leaders for his arrest, touched off protests in which people wore hooded sweatshirts like the one the teenager had on, and set off a furious nationwide debate over race and self-defense that reached all the way to the White House, where President Barack Obama observed: "If I had a son, he'd look like Trayvon."
Separately, the U.S. Justice Department's civil rights division is conducting its own investigation.
Corey said the decision to bring charges was based on the facts and the law, declaring: "We do not prosecute by public pressure or by petition."
One of the biggest hurdles to Zimmerman's arrest over the past month was Florida's "stand your ground" law, which gives people wide leeway to use deadly force without having to retreat in the face of danger.
Corey repeatedly declined to answer questions about details in the case. "So much information got released on this case that never should have been released. We have to protect this prosecution and this investigation for Trayvon, for George Zimmerman," she said.
Tensions have risen in recent days in Sanford, a town of 50,000 outside Orlando. Someone shot up an unoccupied police car Tuesday as it sat outside the neighborhood where Martin was killed. And a demonstration by college students closed the town's police station Monday.
But as the hour of the prosecutor's announcement neared, the Martin family and their lawyer pleaded for calm.
Around the time of the news conference, 37-year-old Jared Towns was walking near City Hall.
"This is not closure at all. It's just charges. We'll see what happens now. I'm happy he was charged. It's good for the family. But they aren't to the justice part of it, yet," he said.
Six weeks ago, Martin was returning to the home of his father's fiancee from a convenience store when Zimmerman started following him. Zimmerman told police dispatchers: "This guy looks like he is up to no good — he is on drugs or something." At some point, the two got into a fight and Zimmerman used his gun.
Zimmerman told police Martin attacked him after he had given up chasing the teenager and was returning to his truck. He told detectives that Martin knocked him to the ground and began slamming his head on the sidewalk. Zimmerman's father said that Martin threatened to kill his son and that Zimmerman suffered a broken nose.
A video taken about 40 minutes after the shooting as Zimmerman arrived at the Sanford police station showed him walking unassisted without difficulty. There were no plainly visible bandages or blood on his clothing, but Zimmerman may have had a small wound on the back of his head.
The local prosecutor disqualified himself from the case, and Gov. Rick Scott appointed Corey, the prosecutor for Jacksonville, to take it over.
Corey has tried hundreds of homicide cases and is known for tough tactics aimed at locking up criminals for long sentences and making it difficult to negotiate light plea bargains. Corey is known in legal circles as being passionate about victims' rights.
She said she met with Martin's "sweet parents" and prayed with them.
"We only know one category as prosecutors, and that's a 'V,'" she said at the news conference, referring to victims, and making a V with her fingers.