Maps on the Kremlin and government websites include Crimea, describing it as the "youngest region of Russia."
Russia's absorption of Crimea has drawn international condemnation and sparked the worst East-West crisis since the Cold War.
Russian troops have seized Ukrainian military bases on the mostly Russian-speaking region of two million people since a March 16 independence referendum.
Several of Russia's most popular websites including the main search engine, Yandex.Ru, have also changed their maps.
But on a parallel site for Ukrainian users, Yandex.Ua, it continued to show Crimea as part of Ukraine.
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Yandex said it would also change the way it presented news, with stories about Crimea being classed as domestic news for readers based in Russia.
The Russian language version of Google shows Crimea with a dashed border line, used for "disputed" boundaries.
Russia's biggest Internet company, Mail.Ru, was one of the first sites to change Crimea to part of Russia on March 21, the day that President Vladimir Putin signed the agreement absorbing the peninsula.
One Russian bank used the change as an advertising opportunity, covering the side of a building in central Moscow with a map of Crimea and the slogan "Russia and Crimea together forever".