The bodies were discovered in a first floor bedroom at about midday on Wednesday – a day and a half after the house in Croxden Way, Eastbourne was set on fire at 1am on Tuesday.
Sussex Police said they are treating the deaths of the previously unaccounted for occupants as murder.
They are treating the incident as arson.
They said they believe the bodies to be of a 34-year-old woman and her four-year-old son.
A 26-year-old man who was also at the house during the fire was taken to hospital with burns in the early hours of Tuesday.
He remains in an induced coma, police said.
They added that he was the woman’s partner but is not the father of the child whose body is believed to have been discovered.
“This is a difficult scene and it will take some time before forensics examinations are complete,” a police statement said.
Detective Chief Inspector Mike Ashcroft, of the Surrey and Sussex Major Crime Team, who is leading the investigation, said: “This is a dreadful incident and the worst fears have been realised.
“Our thoughts are with the victims, their families and the whole community at this time.
“I urge anyone with any information about this or any footage of the fire to contact us.”
:: Anybody with information should call 101 quoting Operation Druffield or reporting it online.