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Charles Horton has resigned as chief executive of Govia Thameslink, the company which runs Southern.
It comes after a host of major problems hit the firm's services following the introduction of a new timetable in May.
That led to significant disruption to passengers and significant controversy for the train operator.
Govia Thameslink Railway (GTR), the UK's largest rail franchise, operates Thameslink, Southern and Great Northern train services.
Southern operates services between Ashford and the south coast and Tonbridge to Redhill.
Between April 2006 and September 2014 he was managing director of Southeastern, which operates services across Kent.
Prior to that, he was MD of Southern for three years.
GTR says Mr Horton will remain in post to oversee the development of a temporary timetable.