The police searched the mosques in Pasing and Freimann, but did not find anything suspicious.
Another mosque in the northwestern city of Iserlohn also received a similar email on Thursday which claimed that explosives had been placed in the building.
Police evacuated the mosque, cordoned off streets in the area, and began searches with bomb-sniffing dogs.
Germany’s largest mosque in the western city of Cologne had also received a hoax bomb threats on Tuesday.
The country has witnessed growing Islamophobia in recent years triggered by the propaganda of far-right parties.
More than 100 mosques and religious institutions were attacked in 2018.
Police recorded 813 hate crimes against Muslims last year, including insults, threatening letters and physical assaults. At least 54 Muslims were injured in the attacks.
Germany, a country of over 81 million people, has the second-largest Muslim population in Western Europe after France. Among the country’s nearly 4.7 million Muslims.