The 51-year-old has tendered his resignation with the club spending the winter break inside the bottom two of the Bundesliga.
"After plenty of consideration and lots of talks, I have come to the conclusion that I will end my work at Hannover 96," said Frontzeck, who guided the club to safety after taking over in April.
"Unity and trust are necessities for successful work, particularly in our situation.
"I no longer felt that I had these at Hannover.
"Avoiding relegation together last season was a great achievement and that was only possible because we united all of our efforts and everybody supported the team and the coaching staff with their faith and confidence.
"I would like to wish Hannover and the team and the enthusiastic fans a successful second half of the season, and hope they avoid relegation again."
Hannover have accepted Frontzeck's resignation.
"I have got to know Michael Frontzeck as a loyal person with a strong character," commented Hannover's director of sport Martin Bader.
"Our survival in May will always remain linked with Michael Frontzeck's name.
"His decision warrants respect and it is now our task to present a new coach before the restart of training on January 4 - somebody who can prepare the team for a demanding second half of the season."