Rodriguez was found in a lagoon in the U.S. territory's capital Saturday, a couple of days after she was reported missing. She was identified Sunday via dental records, Puerto Rico's Institute of Forensic Science said in a statement.
FBI spokeswoman Limary Cruz told The Associated Press that the federal agency was filing charges that would soon be announced.
Verdejo and his lawyers previously declined comment, and police said the boxer did not originally cooperate and refused to answer questions.
Rodríguez's family said she was pregnant with Verdejo's child. Keila Ortiz, the victim's mother, told reporters that her daughter had called her before she vanished Thursday and told her that Verdejo was going to her house to see the results of a pregnancy test.
"I told her, 'Be careful,' because he had already threatened her,'' Ortiz said. She said Verdejo had told her daughter not to have the baby, mentioning his career and family.
Verdejo is married but had known Rodríguez since middle school and kept in touch with her, her parents said. They reported her missing after she didn't show up for her job at an animal grooming business.
Verdejo (27-2, 17 KOs) represented Puerto Rico at the Olympics in 2012, the same year he became a professional boxer competing in the lightweight division. His career was temporarily sidetracked after a 2016 motorcycle accident that put him in the hospital.
The case has outraged many in Puerto Rico, where another woman was recently found burned to death after she filed a domestic violence complaint that a judge dismissed. A Superior Court judge has announced an investigation into that decision.
Hundreds of people gathered on Monday at a bridge that crosses the lagoon where Rodríguez's body was found to demand justice for her and other women killed, with some throwing flowers into the water below.
-AP