Eliezer Marquez Navedo also faces two counts of rape and one count of kidnapping after police said he ambushed the woman while she was jogging in the eastern coastal town of Fajardo.
"He waited for her to pass by and he forced her into the trunk [car boot]," said Antonio Lopez, Fajardo's police investigations chief.
Mr Marquez, who could face up to life in prison, walked into court with his head down for a closed hearing in which the charges were announced. He did not enter a plea and does not have a lawyer yet.
Police said Mr Marquez admitted abducting Sara Kuszak after seeing her jogging alone.
She made a desperate call for help on her mobile phone from the trunk of her kidnapper's car on Wednesday, about an hour before she was found dead. The FBI then used the signal from the phone to help locate the suspect.
Mr Marquez's mother, Ines Navedo, was convicted of slashing the throats of a brother and sister, ages 2 and 3, in 1992, and served seven years of a 26-year sentence before being released on parole with an electronic ankle bracelet for good behaviour.
Relatives of the victims told authorities that Miss Navedo attacked the children because she was angry the family had shunned her hearing that she was HIV positive, said retired police officer Pablo Roman, who investigated the case.
A jury later found her guilty of second-degree murder, because she was under the influence of drugs and alcohol, Mr Roman said.
Miss Kuszak, 35, who moved to Savannah, Georgia, from San Francisco about five years ago, arrived Tuesday night in Puerto Rico, where she met up with her fiance and several friends.
Miss Kuszak, who worked on sailboats and part-time in real estate and catering, was five months pregnant, friends said.
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