Police were checking out a report of a possible trespasser on the 800 block of North Oakland Avenue Sunday when they spotted the altar. No intruder was found.
The bones were turned over to the coroner's office. Police are calling it a case of suspicious circumstances.
"They'll be examined forensically to determine whether or not the bones are in fact human in nature, then the investigation will determine if the bones were obtained in a legal fashion," said Pasadena Police Lt. Ed Calatayud.
Investigators say the couple that lives in the home practices a West African and Caribbean religion known as Santeria, and they are cooperating. Some burned artifacts, along with animal bones, incense and candles were also found at the altar.
So far, no arrests have been made.