The former Privett Park defender has been appointed to lift the club out of the doldrums after a difficult period.
Molyneaux replaces Craig McAllister and Matt Tubbs, who left at the end of the season after Borough narrowly escaped relegation from the Southern League premier division south.
Molyneaux spent four years at Borough during his playing days, making 83 appearances between 2011-2015 before joining the Hawks.
He was part of Gosport’s memorable FA Trophy side that lost 4-0 against Cambridge United in the final at Wembley in 2014.
Since then Borough's fortunes have nose-dived. They have dropped out of National League South and spent the past two seasons battling the drop.
The 36-year-old beat off strong competition to get the job, with more than 30 applicants all showing their interest.
He’s been tasked with returning success to Privett Park – and Iain McInnes is convinced Molyneaux can create a team capable of challenging at the top of the division next season.
The Borough chairman said: ‘I have been very impressed with Molyneaux and he has been here before as a player.
‘He is very knowledgeable at this level of football.
‘I know that he is very keen to get into management and make a success of it.
'He will be bringing in the much-coveted figure of Kevin Braybrook as coach.
‘Changes were necessary because I don't want another season fighting to avoid relegation.
‘We need to be challenging at the top and looking to get promoted back up to National League South.'