A new managing director will run train operator South Central from March.
Current managing director David Franks will be replaced by operations director at the troubled Connex South Eastern Charles Hortin.
Mr Franks is moving to National Express, having run South Central since Govia took over the franchise from Connex in August 2001.
The former station manager at Brighton regularly commutes from his home near Haywards Heath, West Sussex, to South Central's Blackfriars headquarters.
He joined South Central from the award-winning North Western Railway, which is was credited with turning into a successful operation.
When Mr Franks was appointed, he promised to invest more that £1.5 billion improving the service and recruiting additional staff, together with £900 million on new trains.
His move to National Express could be viewed as a promotion as the company owns nine rail franchises compared to Go-Ahead's three.
His replacement, Mr Hortin, has seen troubled times at Connex South Eastern.
In December, the Strategic Rail Authority (SRA) announced that it was bailing out the train company, which runs services between London, Kent and Sussex.
Connex is said to be making enormous losses and its franchise will now finish at the end of 2006 rather than in 2011.
Thameslink will also be affected by the reshuffle, which was announced last night by the Go-Ahead Group - majority partner in the Govia franchise.
Director and general manager at Thameslink Mark Causebrook will become the company's managing director.
Govia development director Tom Smith will become its planning director, overseeing South Central's depot refurbishment project and Thameslink's refranchising.
Keith Ludeman, chief executive of Go-Ahead's rail division, said: "These changes demonstrate our long-term commitment to the industry and further strengthens our management team. We have extensive knowledge of the UK rail business and its complexities and the division is very well-equipped to meet the challenges ahead."
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