The Crown case is that the defendant was so frustrated that Rua the sea lion was stealing fish and ripping holes in his set nets, he killed her.
Prosecutor Craig Power told the jury in opening yesterday that no one would give evidence that they saw Lowery kill Rua the sea lion.
The case would be circumstantial, he said.
On November 5, 2016, Doc biodiversity ranger Jim Fyfe was called out to Portobello after hearing of the animal's death.
He found Rua behind some rocks at Quarantine Point and initially thought she had been shot.
However, when the carcass was examined by experts at Massey University, they found two stab wounds.
An scientist is expected to tell the jury the injuries were inflicted by a smooth-edged blade at least 15cm long.
Police executed a search warrant at Lowery's home while he was on holiday and seized two knives and a bayonet from his kitchen.
That bayonet, the expert will say, was consistent with the wounds found to Rua.
A forensic scientist from the United States analysed the bayonet and found a combination of human and sea-lion DNA, Mr Power said.
Yesterday the court heard from Lowery's daughter and his former partner, both of whom said the defendant told them he was going to kill the sea lion.
The trial continues.