Merritt matched David Frost's tournament mark set in 1994 and topped the leaderboard at 12-under 130, a stroke off the 36-hole event record shared by Jack Nicklaus and Phil Mickelson.
Spieth started off the low, low scoring at Harbour Town Golf Links, making nine birdies in a bogey-free round after struggling Thursday to a 74 in the first round. The 21-year-old Texan was six shots back at six under.
Spieth tied his career low set at the Deutsche Bank Championship in 2013. He has been on a major role the past month, winning the Valspar Championship and finishing second in San Antonio and Houston before capturing his first major title at Augusta National last week.
Merritt had nine birdies over his final 12 holes, finishing with a five-foot putt on the course's signature lighthouse 18th. He had a four-stroke lead over defending champion Matt Kuchar and John Merrick.
Merrick had a 65, and Kuchar shot 66.
Sei Young Kim shot a two-under 70 in wind gusting to 30 mph to take a one-stroke lead in the Lotte Championship at Kapolei, Hawaii.
With the breeze making birdies elusive at Ko Olina, the 22-year-old South Korean player reached 12-under 204 to break out of a first-place tie with I.K. Kim.
Sei Young Kim will take a lead into the final round for the second straight tournament. Two weeks ago, she had a four-shot advantage in the ANA Inspiration and finished fourth in the major championship.
Sei Young Kim won in the Bahamas in February in her second start as an LPGA Tour member.
I.K. Kim was second after a 71. Third-ranked Inbee Park was another shot back after a 69.
The top five are all from South Korea, with Jenny Shin four shots back after a 70, and Chella Choi at seven under after a 71. Defending champion Michelle Wie had five bogeys and four birdies in a round of 73 to fall eight shots back in her home event.
Ian Woosnam was tied for the lead at four under with five holes left when first-round play in the Champions Tour's Greater Gwinnett Championship at Duluth, Ga., was suspended because of rain.
The round was scheduled to be completed Saturday morning at TPC Sugarloaf, followed by the second round. There is more rain in the forecast Saturday and Sunday.
Woosnam, playing in the event for the first time, was tied with Tommy Armour III, Joey Sindelar, Gary Hallberg and Olin Browne. Armour and Hallberg had four holes left, Sindelar three and Browne six.
Defending champion Miguel Angel Jimenez was even par through 11 holes. Bernhard Langer, second last year after winning the inaugural tournament in 2013, was one under through 12.
Only one group completed the first round, with Tom Byrum the clubhouse leader at 3-under 69.
American Peter Uihlein shot a four-under 68 in windy conditions to take a one-stroke lead in the Shenzhen International in China.
Uihlein had a nine-under 135 total at Genzon Golf Club. He won the 2013 Madeira Islands Open for his lone European Tour title.
Thailand's Kiradech Aphibarnrat was second after a 69. Two-time Masters champion Bubba Watson was tied for 42nd at even par after a 74.