The chancellor led 14 delegates for the closed-door talks with seven senior Greens leaders inside a parliamentarians club in rainy Berlin, almost three weeks after elections.
The exploratory talks with the left-leaning ecologist party are part of Merkel's hunt for a governing partner after her conservatives won September 22 elections but fell short of a ruling majority.
Merkel's Christian Democrats (CDU) and their Bavarian partners the CSU are already engaged in ongoing talks with the centre-left Social Democrats (SPD), who are widely seen as the more likely ally.
Doubts seemed to outweigh optimism ahead of the meeting today about such a coalition, as veteran Greens politician Juergen Trittin criticised the Merkel government.
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He spoke of "clear conflicts" between them in energy, climate and eurozone policy and labelled CSU Interior Minister Hans-Peter Friedrich's comments on tougher rules for asylum seekers "an abyss of cynicism" after the migrant deaths on the Italian island of Lampedusa.
Only days ago, Environment Minister Peter Altmaier had told news magazine Der Spiegel that "the chances of a coalition with the Greens have risen in recent days from 'theoretical' to 'conceivable'".
"We want to keep fighting for a more ecological, just and modern country," said Hofreiter.
The Greens, who grew out of the environmentalist, anti-war and anti-nuclear movements, entered parliament in the 1980s, many wearing sneakers and long hair and handing out sunflowers.