After talks at Vladimir Putin's summer home in the Black Sea resort of Sochi, the two leaders appeared together at a tense news conference where they barely looked at each other.
Mrs Merkel urged Vladimir Putin to use his influence to protect the rights of gay people in Chechnya.
"But, I pointed out again how important the right to demonstrate is in a civil society, the importance of NGOs, and I also mentioned again that we have received very negative reports about the way homosexuals are treated in Chechnya, and I asked President Putin to use his influence in order to safeguard the rights of minorities in the same way it has been done with Jehovah's Witnesses."
She raised the issue after harrowing accounts emerged from activists in recent weeks of police in the republic of Chechyna arresting and torturing dozens of gay people.
Such as this one from a man who fled to Moscow after being detained and tortured in Chechyna.
"They have a special black box and they tie wires to your hands or ears and shock you. The pain is awful, you scream, it's terrible torture. They used to detain people before, all the time to blackmail them. The level, it's at now, it's extermination, the extermination of gay men."
Both leaders stressed the importance of the peace deal for eastern Ukraine, known as the Minsk agreement.
The agreement was brokered in the capital of Belarus by Germany and France in 2015, and was signed by Russia, but violence in the region has continued.
Mrs Merkel saying there hasn't been much progress and getting a ceasefire is crucial.
"As chancellor I made clear that we are prepared to do everything to support a ceasefire and to help those people in desperate need. I think that the concept of safety zones is one which should be expanded on and I hope we will also have the opportunity to talk about Libya because that is a big challenge."
On the intractable situation in Syria, Vladimir Putin said there needed to be what he called a thorough and unbiased investigation into last month's chemical attack on the Syrian town of Idlib.
Asked about alleged Russia interference in last year's US election, Mr Putin said Russia never intereferes in the poltical life of other countries.
He described the allegations as mere rumours.
"We never interfere into political life and political processes in other countries and we would very much like that nobody interfered into our political life and into the political life in Russia.You've referred to the US example which is not confirmed by anything or anyone. These are just rumours used in the internal political struggle in the US."
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