The American, 28, hit eight birdies in a bogey-free 64 to lead Sung Kang, with Stewart Cink, Jhonattan Vegas and Kyle Stanley another shot back on six under.
England's Justin Rose shot a five-under 67, with 2015 Masters champion Jordan Spieth two more shots adrift.
England's Luke Donald carded a one-under 71, while compatriots Chris Wood and Andrew Johnston are one over.
"They've done a great job here with conditions around the greens and making it as similar as possible to next week," said Fowler, who will be aiming to win his first major at Augusta.
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Rickie Fowler warmed up for next week's Masters by taking a one-shot lead after the first round of the Houston Open.