The 33-year-old has recently played in the British and Irish Cup for the Dragons Premiership Select side and joins five other personnel changes that have been made to the team.
Commenting on the return of Thomas Rhys Thomas, Director of Rugby Lyn Jones said: "It's a big relief for us to have 'TRT' back.
"He has been appointed captain for his leadership and maturity. We have missed those qualities in our side dreadfully.
"Elliot Dee has played very well and has shown the promise time and time again but at this stage we need to have Rhys back in."
The back line remains unchanged with fullback Carl Meyer joining wings Tom Prydie and Ashton Hewitt. The centre pairing also receives the nod from the coaching staff as Adam Hughes and Adam Warren are selected. The half backs see one change made as fly-half Dorian Jones is joined by scrum-half Sarel Pretorius.
The front row has two changes made to it, as Boris Stankovich is joined by skipper Thomas Rhys Thomas and tight-head prop Brok Harris. Matthew Screech and Rynard Landman remain in the second row, as three changes are made to the back row. Flankers Lewis Evans and Nic Cudd return to the starting XV and are joined by Welsh Rugby World Cup star Taulupe Faletau.
The replacements bench has three changes made to it as Rhys Buckley, Ed Jackson and Charlie Davies join Phil Price, Lloyd Fairbrother, Cory Hill, Jason Tovey and Ross Wardle.
Newport Gwent Dragons team to face Munster
Carl Meyer, Tom Prydie, Adam Hughes, Adam Warren, Ashton Hewitt, Dorian Jones, Sarel Pretorius; Boris Stankovich, Thomas Rhys Thomas ©, Brok Harris, Matthew Screech, Rynard Landman, Lewis Evans, Nic Cudd, Taulupe Faletau.
Replacements: Rhys Buckley, Phil Price, Lloyd Fairbrother, Cory Hill, Ed Jackson, Charlie Davies, Jason Tovey, Ross Wardle.
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