Former Wales international Rees is drafted into the front row and is also handed the captaincy for the encounter at the Irish Independent Park.
Head Coach Danny Wilson makes a total of four changes to the side that narrowly lost out to Connacht.
Lock James Down is called up to the second row alongside Lou Reed who makes his 50
th appearance for Cardiff Blues.
Manoa Vosawai is named at Number Eight and will join forces with flankers Josh Turnbull and Ellis Jenkins in the back row.
The final change to the starting line-up comes on the wing with Garyn Smith selected.
Jarrad Hoeata (calf), Josh Navidi (neck). Aled Summerhill (head), Cory Allen (leg), Tom James (foot), Taufa'ao Filise and Tomos Williams miss the game through injury.
Macauley Cook and Jevon Groves are among the replacements and young wing Harry Davies could his Guinness PRO12 debut after being named on the bench.
Wilson said: “Munster have been very strong so far this season and have some quality players. They have big ball carriers and play a power game - we need to match that.
“We will give them a huge amount of respect away from home, but at the same time we feel we are building something and are hoping that we can gain some momentum and good results in these away games to hold us in good stead for the rest of the season.”
Cardiff Blues: 15 Dan Fish, 14 Garyn Smith, 13 Tom Isaacs, 12 Gavin Evans, 11 Richard Smith, 10 Rhys Patchell, 9 Tavis Knoyle; 1 Sam Hobbs, 2 Matthew Rees (c), 3 Craig Mitchell, 4 Lou Reed, 5 James Down, 6 Josh Turnbull, 7 Ellis Jenkins, 8 Manoa Vosawai
Replacements: 16 Kristian Dacey, 17 Thomas Davies, 18 Dillon Lewis, 19 Macauley Cook, 20 Jevon Groves, 21 Lewis Jones, 22 Gareth Davies, 23 Harry Davies