A 61-year-old Bronx man was arrested late Wednesday and charged with killing his pregnant daughter and burying her body in the basement of a home they shared in the Baychester section, police said.

William Caruth, of 3242 Corsa Ave., was charged with second-degree murder and manslaughter in the death of his 39-year-old daughter, Andrea Caruth, the NYPD said.

The motive for the slaying was not clear, police said. Andrea Caruth’s body was found Wednesday partly buried in the basement of the Bronx home, law enforcement sources said.

Andrea Caruth, who police said was about five months pregnant, was last seen Sunday about 10:30 a.m. in her home.

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Police discovered blood there Tuesday and brought in a cadaver dog, which alerted authorities and helped detectives find the body of a woman in a pit beneath the floor of a furnished basement apartment, said one of the sources, all of whom did not want to be identified.

Andrea Caruth’s body was face down, partly covered with dirt; and the hole, which was in a closet area, was covered with a piece of plywood, the source said. An NYPD spokesman confirmed the identity of the body.

According to the law enforcement officials, Caruth ran a day care center in her home for between 12 and 20 children. She had a boyfriend, who reported her missing, the sources said. They said William Caruth lived in the basement apartment.

Property records showed that the 45-year-old dwelling was valued at $296,000 and was owned by Andrea Caruth, who acquired sole title to the home in 2006.

Family members couldn’t be reached for comment.