Muldoon has played 222 times for his province and returns to a position that he first held from 2009 to 2011.
The 31 year-old from Portumna, Galway joined the Connacht set up in 2001 and made his senior debut for the province in 2004.
The multi-talented back rower recently signed a new two-year contract that will see him play with Connacht until at least the summer of 2016.
Commenting on the captaincy, Muldoon said: "I'm delighted to be named captain this year. It's a huge honour to captain my home province. It's been three years since I was last captain and a lot has changed since then so I'm thrilled to have been asked again.
"I'm excited about leading a great squad in what is a new and challenging season for us."
Connacht Head Coach Pat Lam added:
"John Muldoon is the ultimate Connacht man and the natural choice for captain. His performances last year were of a consistently high standard week in week out which is what you want from your captain.
"John embodies every single one of our values and is someone who demands huge respect on and off the field. For the new and younger players coming in, he leads by example and is the ideal person to guide the team in the new season."
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