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Merrington was a brief caretaker manager for Sunderland following the departure of Jimmy Adamson in 1978, and in 1980 he again took over from Adamson as caretaker manager (for 1 game only) at Leeds United.
He took charge of Southampton for the 1995-96 season and was Premiership Manager of the Month in April 1996, his only full season in management. Despite securing Southampton's top flight status on goal difference, he was dismissed on 14 June 1996 and succeeded by Graeme Souness. During the final weeks of the 1995-96 season, he guided Southampton to two crucial wins which played a big part in their survival - they first beat Manchester United (champions that season) 3-1 at The Dell, and then won their penultimate game 1-0 at Bolton Wanderers, a result which confirmed the other side's relegation.
A year later he returned to the club as a coach under next manager Dave Jones but left again three years later after Jones was succeeded by Glenn Hoddle. His next stop was a brief spell working as Walsall's first-team coach alongside manager Colin Lee in 2002.