The meeting was punctuated by some tension prompted by differences over Russia's rights record, a topic that had been pressed onto Merkel's agenda by German lawmakers.
While Moscow and Berlin have enjoyed generally good relations in recent decades, built on cooperation in practical areas like energy, the relationship appears to have cooled slightly since Merkel took over.
Electoral flaws and a perceived clampdown on dissenters -- including the jailing of punk activists from the group Pussy Riot -- have strained Europe's and the United States' dialogues with Moscow.
In one testy exchange during their November 16 meeting, Merkel said Russian officials should not "consider every criticism as destructive."
"We are certainly irritated...that a whole series of laws was recently passed [in Russia] which I cannot see how they facilitate the freedom of groups to organize or, for instance, to promote themselves," Merkel said.
Russia has tightened laws against unsanctioned protests and dissent, as well as passing a number of local measures aimed at discouraging homosexuals from speaking publicly about their sexuality.
"As for political and ideological issues, we hear our partners," Putin said, "but they hear about what's happening from very far away."
Putin went on to accuse at least one of the Pussy Riot members in jail of participating in an anti-Semitic protest, although his interpretation of that stunt is disputed by the Voina group that organized it.
Putin's press secretary, Dmitry Peskov, said on the eve of Merkel's visit that the Russian president would raise the issue of European legislation "that adversely affects our interests."
Peskov elaborated that meant talks on the European Union's "Third Energy Package," which enforces "unbundling."
Russian gas giant Gazprom objects to the "unbundling" requirement, as it requires a separation of the production, transport, and sale of energy supplies.
Gazprom produces and sells gas and owns its own transportation facilities. It currently provide some 25 percent of the EU's gas needs.
Merkel and Putin also discussed Syria, the ongoing violence between Israel and Gaza, and Iran's nuclear program.