Tauranga Crown Solicitor Greg Hollister-Jones told the court yesterday Boynton had been in a relationship with 16-year-old Ngarangi Wickliffe since late 2009 and assaulted her on several occasions including while she was pregnant with Boynton's child.
Mr Hollister-Jones said Ms Wickliffe suffered several black eyes and a blood nose at the hands of Boynton.
On January 2 last year, Ms Wickliffe gave birth to a boy.
The Crown alleges Boynton started assaulting his infant son because he couldn't cope with him crying.
On one occasion the child was crying in his carseat and Boynton took him out of the car and slapped him in the face, the court was told. The child was given to Ms Wickliffe so she could try and stop him crying. The baby was red and hot and Boynton threw a container of water at him, Mr Hollister-Jones said.
On another occasion Boynton and Ms Wickliffe were at their home when the baby, who was only about 2 or 3 months old, began crying and Boynton is alleged to have shaken his son and slapped him in the face.
Boynton said the child needed to learn before throwing him on a bed several metres away.
Late in April last year Boynton and Ms Wickliffe separated and Ms Wickliffe said she didn't want to leave without her son but Boynton wouldn't let her.
Boynton, his son and children from another relationship went to stay with some friends. The baby was grizzling all day and had been put to bed. Boynton went into his son's bedroom after hearing him crying.
"The accused was only away for about 30 seconds. In that time the Crown say the accused snapped and either shook or slammed [the infant] on to a soft surface," Mr Hollister-Jones said.
In a panic, Boynton ran out of the room, saying his child was not breathing. The child's lips were blue and his eyes rolled back. Emergency services were called and were told the child was dazed but was breathing. Ambulance officers arrived and told the family to treat the boy with panadol, Mr Hollister-Jones said.
After having seizures during the night, he was taken to Whakatane Hospital the next day. He was airlifted to Starship Hospital and it was found that he had bleeding between the skull and brain. Blood vessels in his eyes had also burst.
Medical staff found the child had extensive brain injuries which were the result of "shaking, slamming, throwing or hitting a baby or by a combination of those".
The court was told that on May 18, Boynton attempted to pervert the course of justice by telling a family member to tell Ms Wickliffe "catch you up Ngarangi sieg f****** heil".
In a brief opening statement Boynton's lawyer, Tony Rickard-Simms, said Boynton was no angel but denied assaulting his child and the other assaults on his former partner.
The trial before Justice Ailsa Duffy is expected to take two weeks.