While negotiations with national rail provider Deutsche Bahn were said to be making progress over the weekend, the union has been unhappy with efforts by private rail companies.
“We want equal pay for equal work,” said GDL leader for Berlin, Saxony and Brandenburg, Frank Nachtigall.
Train drivers walked off their jobs at 2:30 am in the northeastern German states.
The action is expected to last 24 hours and will affect providers Abellio, Arriva, Benex, Keolis, Veolia and Hessische Landesbahn, along with their smaller subsidiaries.
Together these companies cover 15 to 20 percent of Germany's passenger service.
Passengers on AKN, Metronom and the Nord-Ostsee-Bahn in particular should expect delays and cancellations throughout the day.
“Due to the strikes the schedule had to be significantly thinned out,” an AKN spokesperson said. “Thousands of commuters, including employees, school pupils and university students are affected.”
Some companies were helping passengers reach their destinations with additional bus service, they said.
Meanwhile the GDL has resumed talks with Deutsche Bahn, with no strikes planned at the national level.
Some progress was reportedly made Saturday in the ongoing dispute, with both sides agreeing to continue talks on April 7 and 8.
The GDL is demanding a nationwide wage agreement to cover all Germany's train drivers, so private companies will be forced to raise wages to match those paid by Deutsche Bahn. The union also wants a five percent wage increase and better redundancy protection guarantees.
"We have a firm agreement that the nationwide train drivers contract will be linked to the Deutsche Bahn's in-house contract," GDL boss Claus Weselsky said after Saturday's talks.
But he added that there was still the outstanding issue of working hours. Deutsche Bahn has agreed to make a compromise offer soon.
There are 26,000 train drivers in Germany, 6,000 of whom work for private companies. Strikes in recent weeks have disabled Germany's rail networks and freight delivery services for several hours at a time.