Former European champions Hamburg have been battling relegation almost every season in the last few years and club bosses said a change was necessary.
"Premature separations with coaches is not something we want. But we believe new impulses are urgently needed in order to reach our goal of staying up," Chief Executive Heribert Bruchhagen said in a statement.
Gisdol had taken over in September 2016. His team narrowly avoided relegation last season but failed to turn things around this season with only two wins in their last 17 league games.
The club said a decision on Gisdol's replacement would be taken very soon.
(Reporting by Karolos Grohmann; editing by Sudipto Ganguly)
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