A possible comeback by the 22-time Olympic medallist has been mooted for a good year with fellow American Ryan Lochte vocal for some time that his friend and rival would return to the pool.
That would appear now to be the case with the Baltimore swimmer having already undergone two doping tests.
USADA said Phelps was among the athletes who underwent doping tests in the period ending September 30.
It means the 28-year-old will be eligible to compete in the trials for the World Championships in Kazan in 2015.
Lochte had brought up the prospect of Phelps returning last year at the World Short-Course Championships in Istanbul.
At the time he told Press Association Sport: "Michael Phelps says he has retired.
"The sport will miss him, he is one of my main friends and rivals and I miss him.
"But I think he'll come back.
"When you do something for so long every day. He is still young, I think he'll be back for Rio."
There has also been talk within the sport that the pair had a wager as to whether Phelps would return.