Fea (18) dominated the senior men's event and won by more than a body length from Nick Tyrrell (Neptune) in 26.22sec.
Tyrrell was timed at 27.76sec and Clive Cox (Waves) was third in 28.05sec.
Fea's win was the highlight of the night for the Queenstown club.
He took the lead out of the blocks and hit the water flying.
It was the second-fastest time of his career.
Fea (18), a butterfly sprint specialist, also won the open 50m butterfly title last year.
His elder brother Josh won in 2006 and 2008.
It was cool to keep the title in the family, he said.
"We don't have any secret. Queenstown just produces the best sprinters."
Fea, the dux of Wakatipu High School last year, has a simple philosophy to racing.
"I don't think about it.
"I just go. It is not hard.
"I knew I was ahead at the start tonight.
"But the race goes so fast and I couldn't tell where I was down the pool and hoped I was still in front."
It was the fastest Fea has raced since the full body suit was banned last year.
His effort pleased his coach, Frank Wylie.
"McGregor's matured a lot in the last two years.
"When he steps up to the blocks he's ready to race," he said.
The Queenstown club brought a record 48 swimmers to the Otago championships and there was a dedication and determination about their performances.
The club is now reaping the benefits of having the local pool opened 12 months of the year.
One of the most promising swimmers in the Queenstown team was Isabella Reid, who won three medals in the girls aged 12 and 13 grade.
She won a gold medal in the 400m individual medley (5min 45.75sec), silver in the 200m breaststroke (3min 08.20sec) and bronze in the 100m backstroke (1min 17.28sec).
It was the first time she had reached the podium at an Otago championships and they were all personal best times.
Two other Queenstown swimmers to impress were Patrick Harris, in the boys aged 12 and 13 100m backstroke, who won a bronze medal (1min 16.71sec), and Lauren Kerr, in the girls aged 14 and 15 200m breaststroke, who won silver (2min 56.50sec).
It was a good night for country swimmers with Kate Holden (Cromwell) winning the girls aged 12 and 13 200m breaststroke (2min 59.59sec), Sydney Cook (Alexandra) the girls 11 and under 200m freestyle (2min 39.90sec), and Jeremy Tasker (Oamaru) the men's aged 14 and 15 400m individual medley (5min 12.20sec).
The championships continue at Moana Pool at the weekend.
