Though the police have not commented, daily Bild reported that they were urgently searching for the 48-year-old father and ex-husband of the murder victims.
Police received a phone tip-off on Monday afternoon of suspicious activity in the cellar of the apartment building in Rosenheim, near the Austrian border. A police patrol then found the body of the woman.
Broadcaster Bayerischer Rundfunk reported that the woman had been bludgeoned to death.
While searching the property, police found the body of the son, aged three.
Bayerischer Rundfunk reported that the boy had been hanged.
The broadcaster also reported that the father was regarded as the chief suspect. It was initially feared that the man had fled with two other children, but they were found safe with relatives.
Bild reported that the ex-husband had been released from prison at the start of this year. His wife divorced him while he was in prison. Since his release, he had harassed and assaulted his ex-wife.
Police and prosecutors are continuing to investigate.