There are currently two separate franchise AREAS (not companies).
South Central (owned by Govia) holds the franchise to operate within the Southern area (using the trading name 'Southern') until 2015. First Capital Connect currently holds the franchise for the Thameslink routes.
A new Thameslink franchise will come into effect from September 2013. Companies will be allowed to tender from October of this year, with the winner being announced in May next year.
Whoever wins the new franchise will initially take over running the services currently operated solely by First Capital Connect. Between April and December 2014, those services currently jointly operated by FCC and Southeastern will be added to the franchise. Then at an (as yet) unspecified date between July 2014 and July 2017 the existing Southern services will be taken over by the Thameslink franchise.
So, eventually, there will be a SINGLE franchise replacing both the Southern and Thameslink ones, but nobody yet knows who will be running it (since the bidding process hasn't even opened).
http://assets.dft.gov...slink-ojeu-notice.pdf
Chris