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Duffy has left his role at the struggling National League North club less than three following the ‘mutual termination’ of his contract.
The Sandgrounders announced Duffy’s departure in a brief statement, saying: “Southport Football Club can confirm that Mark Duffy has left his position as first team manager following the mutual termination of his contract.
“The club would like to thank Mark for his efforts and wish him all the best for the future.”
The former Rovers midfielder initially took caretaker charge following another ex-Tranmere player Neil Danns’ departure in early September after a poor start to the season, having served as his assistant since May 2025.
Danns left his role as assistant manager at Tranmere when he was appointed manager at Southport.
The Sandgrounders currently sit 22nd in National League North with just two wins from their opening 12 games.