A day after matching his career-low score with 12-under 60 at La Quinta Country Club, the 48-year-old Mickelson had a 68 on PGA West's Nicklaus Tournament Course to reach 16 under.
The Desert Classic is the only PGA Tour event to yield two sub-60 rounds.
Mickelson's opener also made him the only player in PGA Tour history to shoot 60 or lower three times, and he is now in prime position to collect his 50th professional title - 28 years after winning his first while still an amateur at the Northern Telecom Open.
The tournament victor in 2002 and 2004, Lefty will play the final two rounds on PGA West's Stadium Course. "I just have to keep that going the next couple of days". He added a birdie on the par-4 ninth for a front-nine 30, and birdied the par-4 10th, par-5 11th, par-5 13th and par-4 14th, holing a chip from in front of the 14th green.
"It's very hard to start a round and go low like this and then follow it up because the expectations are that anything short of a victory is a failure", Mickelson said. Marino had five birdies and an eagle hole-in-one on the par-three seventh on the way to a seven-under par 65 at the La Quinta course.
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"That was an interesting shot because I could have easily lost one and I ended up picking one up", he said.
"I was aware of it", Mickelson said. He won the World Golf Championships-Mexico Championship previous year for his 43rd PGA Tour title and first since the 2013 British Open.
Australia's Curtis Luck was alone in third after firing a bogey-free round of eight-under 64. If Thursday is an indication of how Lefty is feeling coming into the year, then I'm going to have to go change a few predictions. "That's not an easy hole for me, that shot the way it sits along the water".
"I feel uncomfortable right now because I don't know them well enough and I've been trying to get a seminar to learn them all, and I just haven't had time or a chance to", he said.
Prior to the round Mickelson had said on Twitter he was excited to start the season but was "a bit rusty", and even after his flawless display he said he did not feel at his sharpest on the foggy and wet course. "So we thought it was in, but it wasn't like a hundred percent sure and luckily we went up there and it was in the hole". He's the first No. 1 player to play the tournament since the world ranking began in 1986. "I just kept feeding off it and tried to keep the pedal down".