The Supreme Court trial of the man accused of murdering Queensland teenager Daniel Morcombe has begun hearing final submissions.

Brett Peter Cowan has pleaded not guilty to abducting and murdering the schoolboy on the Sunshine Coast in 2003.

The 13-year-old boy disappeared while waiting for a bus under the Kiel Mountain Road at Woombye on December 7 that year.

In August 2011, Cowan was charged with murder, indecent treatment of a child, and interfering with a corpse.

Cowan has pleaded not guilty to all charges.

Brett Peter Cowan. Photo: AAP

In his closing address today, crown prosecutor Michael Byrne QC told the jury there was no evidence to explain how Cowan came to know where Daniel’s remains and clothes were.

“He knew where these things were because he was the one who killed Daniel Morcombe and put them there,” Mr Byrne told the court.

Mr Byrne told jurors they should draw the inference that “Brett Cowan acted with murderous intent to kill”.

He says evidence about a blue car is either mistaken or irrelevant.

Mr Byrne says most witnesses probably saw what they say they saw, but it had not had anything to do with Daniel Morcombe.

Over the past four weeks, the court has heard several recorded alleged confessions by the accused.

The hearing was told a massive police operation was set up to record an alleged confession by the accused.

The court heard undercover officers befriended Cowan on a plane on the day he gave evidence at a coronial inquiry into the teenager’s death.

More than a dozen witnesses also told the hearing they saw a boy and a man standing under the Kiel Mountain Road overpass the day Daniel disappeared.

Cowan has declined to give evidence.