The GDL train drivers' union started its main strike in the early hours, while cargo train drivers walked out Tuesday evening.
The long-running row over train driver pay and working hours flared up again following a three-week truce over Christmas.
The union wants a reduced working week for its shift workers, from 38 to 35 hours, on current wages.
National rail operator Deutsche Bahn has offered flexibility on working hours but refused to reduce them without a pay cut.
Claus Weselsky is head of Germany's GDL Train Drivers' Union.
"We are demanding a staggered reduction in weekly working hours with compensation equalisation."
Deutsche Bahn argues the union's demands would lead to a 50% hike in staffing costs.
The strikes have forced the train operator to run only stripped-back emergency timetables.
Anja Broeker is a Deutsche Bahn spokesperson.
"The strike by the train drivers' union GDL has had a massive impact on train services in Germany, both passenger and freight. We have had to take a massive number of trains off the tracks. According to an emergency plan, we have been running around 20% of our passenger services since two a.m."
The train strikes add more travel chaos in Europe's largest economy, which is also dealing with protests by farmers over subsidy cuts.
Convoys of tractors blocked roads earlier this week and affected traffic.
