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Adam Birchall scored for the first time since the opening day of the season to earn Dartford their second successive home win in The Skrill Premier.
The on-loan Gillingham striker netted what proved to be the winner on 32 minutes as the Darts produced the ideal riposte to their 5-2 defeat at Grimsby in midweek.
Southport skipper Jamie Milligan hit the woodwork early on before Danny Harris forced a good save from Sandgrounders keeper Danny Hurst.
Birchall then headed a Ryan Hayes cross against the bar and Southport scrambled the ball behind. Lee Noble swung over the resulting corner and Elliot Bradbrook had an effort cleared off the line before Birchall snaffled the rebound to make it 1-0.
The visitors looked to get back into a scrappy game, with Karl Ledsham and Chris Almond both calling Darts keeper Alan Julian into action.
At the other end, substitutes Max Cornhill and Uche Ibemere both went close to doubling Dartford's lead but Hurst kept out their efforts.
Victory lifted the Darts up to 17th. They travel to Gateshead on Saturday.