Phelps, the most successful and most decorated Olympian of all time with a total of 28 medals, compared the problem of athletes like Thomas to doping in order to secure a competitive advantage in the pool.
Speaking to CNN, Phelps was firm that something needed to be done about current NCAA guidelines that let Thomas compete against swimmers born female - but could not convey any precise ideas.
"I think this leads back to the organizing committees again because it has to be a level playing field. That's something that we all need. Because that's what sports are. For me, I don't know where this is going to go. I don't know what's going to happen.
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Phelps, who also holds the all-time record for Olympic gold medals at 13, said he simply wants to see fairness across the sport.
"I believe that we all should feel comfortable with who we are in our own skin, but I think sports should all be played on an even playing field," he said.
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"I don't know what it looks like in the future. It's hard. It's very complicated and this is my sport, this has been my sport my whole entire career, and honestly the one thing I would love is everybody being able to compete on an even playing field."
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The NCAA says it plans to study its current guidelines for male-to-female trans athletes on Thursday but has not stressed whether changes might occur.
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As of now, trans women can compete against any other female athlete if they've experienced testosterone suppression treatment for a year. But critics say that it is not enough - as proved by spectacular wins such as Thomas's - and that trans athletes retain substantial advantages over female rivals because of their height and musculature.
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None of Thomas' fellow swimmers have expressed their thoughts publicly on the matter, but some have spoken out anonymously to air their concerns, saying that Thomas is smug, her teammates are mad- and that their coach is just obsessed with winning.
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"She compares herself to Jackie Robinson. She said she is like the Jackie Robinson of trans sports," one of Thomas' teammates told the Washington Examiner. Robinson was the first black baseball player to compete in the Major League.
"She laughs about it and mocks the situation. Instead of caring or showing that she cares about what she's doing or what she's doing to her teammates, she's not sympathetic or empathetic at all. Lia never addressed our team. She never asked if it was OK. She never asked how we felt. She never tried to explain how she felt. She never has said anything to us as a group. She never addressed anything."
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