Kisner, who led by a shot after 54 holes of last year’s US PGA before finishing seventh, carded a five-under-par 66 to secure a one-shot lead over compatriot Tony Finau and the South African pair of Erik van Rooyen and Zander Lombard.
McIlroy, who is seeking a first major title since 2014, was part of a large group on two under par that also included Spain’s Jon Rahm, world No 2 Justin Thomas, 2015 winner Zach Johnson and the English pair of Yorkshireman Danny Willett and Matthew Southgate.
Tiger Woods had arrived at the course with Kinesio Tape visible on the back of his neck, a worrying sign given the 42-year-old’s litany of injury problems in recent seasons.
But although the 14-time major winner visibly winced after hitting his opening tee shot, that appeared to be the result of getting some dust from the dry ground in his eye and he went on to make an ideal start with a birdie from 10 feet.
Woods, who has not won a major since the 2008 US Open, also birdied the fourth and followed a bogey on the 10th with another birdie from 35 feet on the next, but dropped shots on the 13th and 15th and had to settle for a level-par 71.
“I thought I played a pretty solid round and unfortunately didn’t take care of both par-5s and hit eight iron to both of them,” said Woods, who described his stiff neck as “no big deal”.
“The round could certainly have been a little better,” he added.
Kisner is sharing accommodation with defending champion Jordan Spieth, Thomas, Jason Dufner, Johnson, Jimmy Walker – with eight major titles between them – and Rickie Fowler, with only Fowler and Kisner among them still seeking their first major success.
But while Spieth slipped from three under to one over by dropping four shots in the last four holes, including a trip into the Barry Burn on 18, Kisner had no such problems thanks to an eagle, four birdies and a solitary bogey.
“It’s not intimidating at all,” said Kisner, who also shared Spieth’s plane home after his victory at Royal Birkdale last year, of his housemates. “They’re all great people. That’s the best part about it.”
Van Rooyen, who failed to convert a four-shot lead after 54 holes of the Irish Open a fortnight ago, carded five birdies and dropped his only shot of the day on the tough closing hole.
“It was playing as easy as it was going to play this whole week [in the morning], no wind at all, so you had to go out and take advantage of it,” said van Rooyen.
“I was obviously a little nervous, you know, but that’s natural. I’m really proud of how I handled it.”