Some demonstrators held placards saying "I will not forget" to mark the genocide, which virtually obliterated the ancient Hellenic community on the Black Sea coast and claimed the lives of more than 350,000 people between 1916 and 1923.
"We are holding a peaceful protest today and are calling upon the Turkish authorities to recognize the crimes and apologize for their atrocities," a representative of Greek communities in Russia said near the embassy, which is surrounded by police.
More than 500,000 Pontic Greeks live in Russia and former Soviet republics, and the representative said the Turkish authorities should recognize the genocide given its ambition to join the European Union.
"We are not putting forward any political demands," he said. "But if Turkey wants to be considered a European country, it has to take this step."