The organisations have signed an agreement which will involve Otago United players providing coaching and being available for promotional activities for Footballsouth's junior club programme.
The agreement is a sort of thawing in a relationship which has seen the two bodies operate completely independently of each other despite the obvious crossover.
Both Otago United chairman Phil Cunningham and Footballsouth general manager Bill Chisholm recognised mutual benefits from a closer working relationship.
"It would be fair to say we haven't worked together that closely with each other before," Chisholm said.
"But we are trying to work in more of a partnership. Otago United are taking positive steps to reach out to the community a bit more and that is what we are trying to do ourselves."
Cunningham agreed.
"Both organisations realise that if we want football to go ahead in the area everyone has to work together," Cunningham said.
"I think this is a great example that things are heading in the right direction."
Both organisations will have board members attend each other's respective meetings.