She filed the paperwork just days after she said in an interview aired exclusively on ABC News that the ordeal of the trial had put a strain on their marriage.
The petition says the couple, married in 2007, "separated on Aug. 13, 2013 and are not presently cohabiting as husband and wife. The marriage between the parties is irretrievably broken." They have no children.
Shellie Zimmerman, 26, has asked for "equitable distribution" of their assets as well as their debts. She also seeks sole custody of their two dogs, a Rottweiler named Oso and a smaller dog named Leroy.
She filed for divorce Thursday in Seminole County, Fla.
According to the financial disclosure form, she said she is unemployed. She listed her monthly expenses as $755. The couple owes $3,700.20 on their 2011 taxes, according to the form.
Since they separated, George Zimmerman has given her $4,300 for living expenses and the "source of funds appears to be Zimmerman Legal Defense Fund," according to the financial disclosure form.
Shawn Vincent, a spokesman for George Zimmerman's legal team, said there would be no comment.
George Zimmerman's brother, Robert, tweeted, "Pray 4 them."
Shellie Zimmerman pleaded guilty last month to perjury for lying about the couple's finances when the judge was setting bail for her husband. She appeared in court without her husband.
She said in the interview with freelance journalist Christi O'Connor that she felt "very much alone" without him in the courtroom to support her when she pleaded guilty.
During the interview, Shellie Zimmerman said she is "going to have to think about" whether she stayed married to George.
After George Zimmerman, 29, was charged with murder in Martin's 2012 death, the couple was inundated with death threats, went into hiding and had to live with security guards.
"We have been pretty much like gypsies. … We've lived in a 20-foot trailer in the woods, scared every night that someone was going to find us and that we'd be out in the woods alone and that it would be horrific," she said.
Shellie Zimmerman said that on the night that Martin, 17, was killed, she was not at their home because she and her husband had had an argument and she had left to stay with her father.
Despite the tension in their marriage, Shellie Zimmerman said she believes her husband's story that he shot and killed Martin in self defense, and said the most hurtful thing she experienced was hearing that he was a "murderer or some sort of racist."
Shellie Zimmerman must serve 100 hours of community service and one year probation for her perjury.
George Zimmerman was also in the news this week when he was pulled over for speeding Tuesday for a second time this summer.