Also charged was a nurse who can be seen on the tape watching as guards repeatedly kneed and hit Martin Lee Anderson during a 30-minute scuffle on Jan. 5. Guards said the boy was uncooperative and had refused to participate in exercises.
The teen collapsed in the exercise yard at the camp in Panama City and died at a hospital the next day.
The death sparked protests at the state Capitol and led to a shake-up in Florida's criminal justice system and the resignation of Florida's top law enforcement officer.
If convicted, the former guards and the nurse could get up to 30 years in prison. Bail was set at $25,000 each.
Nurse Kristin Anne Schmidt did not show up for an initial appearance Tuesday, and her attorney did not return a phone call from The Associated Press.
Bob Pell, an attorney for former guard Joseph Walsh II, said: "I was hoping cooler heads would prevail, but we will deal with this as it comes down. We understood the political pressure that was brought to bear."
Waylon Graham, attorney for Lt. Charles Helms, the highest-ranking officer charged, said that he had long anticipated charges and that Helms' family has saved money for bail.
Anderson had been sent to the boot camp for violating probation in a theft case. Boot camps often use grueling exercise to instill discipline in juvenile delinquents.
An initial autopsy found Anderson died of complications of sickle cell trait, a usually benign blood disorder. But after an uproar and cries of a cover-up, a second autopsy was conducted by another medical examiner, and it concluded Anderson suffocated because of the actions of guards.
Dr. Vernard Adams, who performed the second autopsy, said the suffocation was caused by hands blocking the boy's mouth, as well as the "forced inhalation of ammonia fumes" that caused his vocal cords to spasm, blocking his airway.
The guards said in an incident report that they used ammonia capsules five times on Anderson to gain his cooperation.
"Today is a good day for me," said Gina Jones, Anderson's mother. "I'm finally getting justice for my baby."
Benjamin Crump, the lawyer for the boy's parents, who have been demanding for months that the guards be charged with murder, said the videotape leaves no doubt the guards are guilty.
"You wouldn't do this to your dog," Crump said. "Stuffing ammonia tablets up his nose, pulling his neck back, covering his mouth."
In April, college students staged a two-day protest in Gov. Jeb Bush's office. The Revs. Jesse Jackson and Al Sharpton joined the students and Anderson's parents for a march on the Capitol.
Florida Department of Law Enforcement chief Guy Tunnell, who started Bay County's boot camp when he was sheriff there, resigned under criticism after he compared Jackson to Jesse James and Sen. Barack Obama, D-Ill., to Osama bin Laden in an agency meeting.
Bush signed a bill in May to replace Florida's boot camps with programs that offer job training and counseling and prohibit physical discipline.
Anderson's family has sued the state Department of Juvenile Justice, which oversaw the boot camp system, and the Bay County Sheriff's Office, which ran the camp. The family is seeking more than $40 million.
"We also hope that once the process is completed that Martin Lee Anderson's family will have the answers to the questions that they legitimately have," the governor said.