The US Attorney’s Office said that Mr Verdejo was being charged with kidnapping and carjacking resulting in death and with intentionally killing an unborn child.
It alleges he then bound her arms and feet with wire and tied a heavy block to her before throwing her off a bridge at 8.30am on Thursday.
The complaint states that Mr Verdejo then shot at Rodríguez’s body as he stood on the bridge.
The complaint says a witness it did not identify helped Mr Verdejo kidnap and kill Ms Rodríguez.
Ms Rodríguez was found in a lagoon near the US territory’s capital on 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.
Mr Verdejo and his lawyers previously declined comment, and police said the boxer did not originally cooperate and refused to answer questions.
Ms 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 on Thursday and told her that Mr 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,” Ms Ortiz said.
She said Mr Verdejo had told her daughter not to have the baby, mentioning his career and family.
Mr Verdejo is married and has a young daughter 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.
Mr Verdejo (27-2, 17 knockouts) 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 yesterday at a bridge that crosses the lagoon where Ms Rodríguez’s body was found to demand justice for her and other women killed, with some throwing flowers into the water below.
Lifeline 13 11 14; Mensline 1300 789 978; Kids Helpline 1800 551 800; beyondblue 1300 224 636; Domestic Violence Line 1800 65 64 63; 1800-RESPECT 1800 737 732
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