Although the party could keep the majority in the state parliament (Landtag), this result is 11.3 points less than its performance there in 2013.
The party's state leader, Volker Bouffier, called the outcome "very humbling".
Chancellor Merkel's party is projected to be down around 10 percent, as are the left-liberal SPD - traditionally the rivals of the supposedly "centre-right" CDU but now working with them in a so-called "grand coalition" after both parties haemorrhaged support in the first federal election since the onset of the migrant crisis in 2015. "We haven't heard about serious contenders to replace her". Meanwhile, the anti-establishment Alternative for Germany party, which advocates a stricter migration policy, has entered Hesse's Landtag for the first time with 13.1% of the vote and now holds seats in all of Germany's regional parliaments. The latter was vying with the SPD for second place after its best result in the state's history.
According to projections updated around 8pm, Ms. Merkel's CDU remained the strongest party in Hesse. After that vote, Merkel allies blamed the CSU's rightward lurch on immigration for its poor results.
Supporters of the Green party celebrate after the state election in the German state of Hesse in Wiesbaden, western Germany, Sunday, Oct. 28, 2018.
The pro-business Free Democrats were seen winning above 7 per cent and the Left Party around 6.5 per cent.
German Chancellor Angela Merkel has told her CDU party that she will not run for re-election as its chairwoman in December, sources say.
Had the party relinquished control in Hesse, some analysts saw her as vulnerable to an intraparty challenge. CDU leaders will meet next Sunday to prepare for a summit in December where party members will vote for a new chairman.
The results in Bavaria and Hesse mirror political trends nationwide.
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The CDU has ruled Hesse for the last 19 years and just won the election at the weekend.
But only the Greens, who are in opposition nationally, are benefiting in polls.
After federal elections in September 2017 defined by sharp drops for both the centre-right and left and the appearance of the far-right in the Bundestag (parliament) for the first time, the SPD agreed only reluctantly to back Merkel yet again.
Rossteutscher said the SPD will be reluctant to bring down Merkel's Government because party leaders know that if they do, and early elections are called, the SPD "would be the biggest loser".
The center-left Social Democrats (SPD) also suffered heavy losses on Sunday, drawing 20 percent of the vote, down by more than 10 percentage points from the last election in 2013.
The result means the anti-immigration party, which entered the federal parliament for the first time a year ago, is now also represented in all 16 German regional assemblies.
"The election was a success on all fronts", said the AfD's leader in Hesse, Jörg Meuthen.
The protest party is expected to eat into both the CDU and SPD's vote to enter the Hessian legislature with a low double-digit share.