The RMT union is balloting more than 1,000 members who work at stations.
GTR, which includes Southern and Great Northern, plans to close 34 station ticket offices and staff 49 others only at peak times.
The two sides are in a long-running dispute over the role of conductors.
Stations listed for reduced ticket office hours include Chichester, Crawley, Dorking, Huntingdon, Hove, Lewes, Reigate, Stevenage, Welwyn Garden City and Worthing.
Ticket window closures include Alexandra Palace, Caterham, Cricklewood, Lancing, Purley and Sutton.
GTR said new "station hosts" would work on the concourse instead to assist passengers and help sell tickets.
The RMT claimed 130 station jobs were at risk and said the cuts would also have a "devastating" impact on safety and services offered to passengers.
RMT general secretary Mick Cash said: "These plans fly in the face of the response from the thousands of passengers who objected to the closure of ticket offices and the de-staffing of stations as Govia drives on with plans for a "faceless railway" where the public are left to fend for themselves on rammed-out, dangerous and unreliable services."
But GTR director Keith Jipps said: "The RMT's threat of further industrial action is entirely unwarranted and clearly another bid by the union to disrupt passengers and GTR across as many parts of our franchise as possible."
"Our new station hosts will be paid more, be able to work in safety and provide passengers with better customer service, but the RMT is not concerned with improving the experience for passengers and are dismissing significant improvements to the terms and conditions for staff," he added.
The union is to ballot staff in the first two weeks of August on "strike action and action short of a strike."
GTR's franchise covers four railways: Southern, Gatwick Express, Thameslink and Great Northern.

Claire Jenkins, 36, of Gowerton, was given the fine after leaving bread crumbs on a bench in Oxford Street, during a Christmas shopping trip.
She said: "I found it degrading. I didn't know it was classed as an offence."
Swansea council said a new campaign was responding to complaints people were being "plagued by seagulls".
"Posters have been put up on bins in the city centre advising shoppers of the penalties for littering and our message is that if you don't drop litter you won't face the fine," a spokesman said.

A recording, which a US website claims was Gibson on the phone to Oksana Grigorieva, has emerged. He is allegedly heard verbally abusing her.
Los Angeles County Sheriff's Department spokesman Steve Whitmore said officers will "review" the recordings as part of an investigation.
A spokesman for Gibson has declined to comment on the claims.
"Anything that is connected to the case we will investigate," Mr Whitmore said.
Last week, RadarOnline.com posted a recording which it claimed was Gibson.
A man can be heard telling Grigorieva he thought she was dressing too provocatively using explicit and offensive language.
At one point, Grigorieva accuses the man of "hitting a woman when she's holding a child in her hands". He replies that she "deserved it".
Gibson and Grigorieva are currently battling each other for custody of their 8-month-old daughter.
The Lethal Weapon and Braveheart star previously hit headlines over an angry outburst in 2006.
Then, a leaked police report quoted him making anti-Semitic comments to a Jewish police officer, who was arresting him for drink driving.
Britain's largest rail franchise, Govia Thameslink (GTR) is facing the threat of more industrial action, in a fresh dispute over planned cuts to ticket offices.
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A woman has been fined £50 for feeding pigeons in Swansea city centre after a council crackdown.
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US police have said they are evaluating claims that Hollywood star Mel Gibson allegedly hit his ex-girlfriend.