The 19-year-old centre has played most of his rugby for Llanelli this season and is a highly-rated member of the Scarlets academy.
Wales begin their campaign at home to Italy on January 31 and coach Byron Hayward believes Hughes is the right choice to lead the side.
"The choice of Steffan, as captain was first and foremost as a result of his experience as a key member of last year's successful side and the leadership he showed as a young player last season," he said.
"He was a leader in our defensive system, but he is also a leader off the field. He is a true professional, very diligent and sets standards. He will no doubt be helped by the other experienced players, in the front row especially.
"We are starting from scratch to a certain extent but we are all looking forward to the challenge.
"We have learned a lot as a management team over the past two years and while our firm objective is to win every game, it's vital we use the Six Nations to develop strength in depth as we prepare to travel to New Zealand for the Junior World Championship."
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