The mother and father of a 3-year-old Bronx girl are facing murder charges after their daughter died of “chronic neglect” and malnourishment, Bronx prosecutors said Tuesday.

Essence Gill-Harris’ parents called 911 after the little girl began having trouble breathing inside her family’s E. 215th St. apartment near Paulding Ave. in Williamsbridge back on March 3, officials said.

Medics rushed the toddler to Montefiore Medical Center, where she died shortly after arriving. Essence’s brother was also found severely malnourished and had to be hospitalized for one month, officials said.

A law enforcement source with knowledge of the case said both children were kept in a crib at all times and “left to fend for themselves.”

Conditions in the home were “not ideal,” the source added.

The city’s Medical Examiner ruled Essence’s death a homicide due to acute and chronic neglect, including malnutrition and dehydration, officials said.

Calvin Harris, 37, and Essence’s mother, Ymonzherae Gill, 35, were indicted on second-degree murder and first-degree manslaughter charges in the girl’s death. They were also hit with assault charges for the neglect of their son, prosecutors said.

“These precious children were found in deplorable conditions,” said Bronx D.A. Darcell Clark. “Sadly, the little girl could not be saved. These defendants allegedly failed to adequately feed and care for their children. They will be held accountable for their actions.”

Gill was arraigned on the indictment in Bronx Supreme Court on Monday. A judge ordered her held on $500,000. Harris was arraigned on Tuesday and ordered held without bail, prosecutors said.

Both are due back in court on Dec. 9.