The 24-year-old has signed for an undisclosed fee, penning a two-year contract with the Shrimps.
Having previously played for Dorchester Town, Sutton United and Havant and Waterlooville, Ayunga joined Bristol Rovers last season.
He made 35 appearances in all competitions, scoring three goals in the process.
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He told the club website: “I’m happy to be here, my first day went well and I’m looking to get settled in.
“It’s happened very quickly, three or four days ago I had no idea it was going to happen!
“I had a chat with the gaffer here and he’s convinced me to come, he said he’s been aware of me for a couple of years.
“It was good to make my League One debut last year and get a good amount of games, so knowing what it takes is what I’m going to bring to the team.”
Ayunga becomes the 14th signing of a busy summer for Morecambe manager Stephen Robinson.
With the club’s first fixture in League One coming a week on Saturday, he is pleased to have added Ayunga to the ranks.
He said: “I’m delighted, Jonah’s a boy I’ve kept tabs on since Bristol Rovers signed him and he has a lot of good attributes.
“He is a big, strong boy, he can run in behind, and there are aspects of his game we know we can improve, he’s still young and there’s a lot of potential in him.
“I’m trying to get two in every position and within our budget it’s difficult, but we’ve managed to do that in a short space of time. People are starting to gel and understand, and I think Jonah just adds to that.”
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