The president's own words more than a year ago — "If I had a son, he'd look like Trayvon" — are fueling the push for his Justice Department to bring federal charges against Zimmerman, the Hispanic neighborhood watch coordinator who has become a symbol of a broken justice system in the eyes of civil rights groups.
When Obama waded into the controversy in March 2012, his words seemed to carry limited consequences. His statement of support for the Martin family played well with supporters and was more than a year away from the polarizing trial.
It's not that simple anymore.
In an apparent effort to cool emotions, Obama reminded Americans after the verdict that the "jury has spoken." And White House press secretary Jay Carney, answering questions for the first time about the outcome, insisted that Obama had "no opinion to express" about a potential civil rights case against Zimmerman.
However, the president's political headache is just beginning.
Attorney General Eric Holder vowed that his department would root out any racial stereotypes causing violent confrontations, telling both a black sorority in Washington and the NAACP in Orlando that his office was not done investigating the shooting inside a gated community in Sanford, Fla. Federal prosecutors started an examination of the killing last year, and the longer it goes, the more questions emerge about whether the Justice Department has enough evidence to bring a case.
Despite White House efforts to distance the president from the department's investigation, Obama inevitably will have to answer for how his administration proceeds. The White House can ill afford to give critics more ammunition as the administration fends off attacks about the IRS' targeting of conservative groups, the postponement of a major part of Obamacare and the Justice Department's spying on journalists.
Republicans were quick to blame the president for his current political conundrum.
"The president has put himself in a very uncomfortable position; both he and Holder have upped the ante," Republican consultant Patrick Griffin said. "The president in the beginning needlessly exacerbated the issue -- it added nothing to the tragedy. I don't see how this ends well for anybody."
The Zimmerman-Martin episode wasn't the first time Obama intervened when racial hostilities boiled over.
In 2009, Obama accused the police officer who arrested Harvard professor Henry Louis Gates inside his own home of acting "stupidly." When more facts emerged, Obama dialed down his remarks and hosted a "beer summit" at the White House between the two men, looking to put the embarrassing situation behind him.
Multiple administration officials scoffed at the notion that Obama has backed himself into a corner on the Zimmerman case. They say the president would have looked out of touch had he ignored an issue igniting so many emotions nationwide.
Opening a civil rights case against Zimmerman would be risky for the Obama administration, as the Justice Department would certainly face complaints of double jeopardy and potential blowback from Hispanics who might feel Zimmerman is being unfairly targeted. If he does nothing, Obama's African-American base would likely accuse him of shying away from what they view as an extreme case of injustice.
In essence, federal prosecutors would have to prove that Zimmerman had racial motives for shooting Martin, a subject that was hardly broached in the Florida trial. And the FBI interviewed dozens of Zimmerman's acquaintances last year and found no evidence that race played a role in the confrontation between the two men.
Some legal experts expect Obama to stay as far away from the political lightning rod as possible.
"I wouldn't go there," said a Justice Department official who served in President George W. Bush's administration, cautioning against a civil rights case against Zimmerman. "It's an incredibly high standard to meet, and it's turned into such an explosive political situation. I would be stunned if they pursued a case."