Whitson set the record for most cumulative days in space, surpassing Astronaut Jeff Williams' record of 534 days.
Whitson said it's a "huge honour to break a record like this", and that it would not have been possible without the support of NASA.
In a dramatic call from the White House on Monday (Tuesday NZ Time) with a pair of astronauts at the International Space Station, Trump urged NASA to speed up its exploration timeline to get humans on Mars "at worst, during my second term".
Whitson, who said she was inspired to become an astronaut by NASA's Apollo program, also joined the president in discussing the goal of sending astronauts to Mars. Trump thanked Whitson on behalf of the American nation and the world.
Ms Whitson was already was the world's most experienced spacewoman and female spacewalker and, at 57, the oldest woman to go into space.
She holds the record for most spacewalks by a female and now the most days in orbit by an American.
Via a video link that was set up between the Oval Office and the International Space Station, President Trump was able to communicate with Whitson and her fellow crew member, Jack Fischer.
In the call to the International Space Station, the president asked Whitson to talk about some of the things they are working on. His daughter and close adviser, Ivanka Trump, also offered congratulations to Whitson from the Oval Office. Peggy remained in the ISS for six months, and during her tenure, she installed a range of important system technologies.
Her fellow USA astronaut Jack Fisher arrived at the ISS last week for the first time.
Ivanka Trump emphasized that Whitson, a biochemist, and Rubins, a biologist who studies cancer, were women who had excelled in math and science. Regardless of what Trump wants for his first "or at worst, during my second term", a NASA journey to Mars is likely more than a decade away, so the astronauts who will take that journey are likely in school right now. She said she used a device the size of a cellphone for the job, and noted that such sequencing can detect microbes aboard spacecraft and monitor astronaut health. "Well, that's good, I'm glad to hear that", he replied.