The draft legislation has been criticised by civil rights activists and internet providers as an attempt to introduce censorship of the Russian segment of the internet.
"Wikipedia community protests against censorship, which threatens free knowledge opened for the mankind," Wikipedia said in a statement on its Russian-language website.
"We ask you to support us in the fight against this bill," it said.
The site is expected to stay offline for 24 hours.
The idea of the blacklist originated last year from Russia's League of Internet Security after the internet watchdog said it had broken up an international ring of 130 alleged paedophiles circulating material via the internet.
According to the draft document, the unified roster of banned websites will be run by a federal agency to be appointed by the government.
The agency will have the right to add items to the blacklist, as will the courts, which already have the authority to ban extremist and other content that violate Russian legislation.
The supporters of the blacklist believe it would curb the spread of online pornography and extremist propaganda.
However, opponents of the idea insist that the current version of the bill cannot be an effective tool for rooting out illegal content and stopping its spread on the internet, as it will not prevent "dirty" users from migrating to other domains and IP-addresses.
Wikipedia went offline for 24 hours in a similar action Jan 18 in a protest against US anti-piracy legislation that could lead to censorship. As a result of blackout protests on thousands of internet sites, the US Congress has postponed the vote on two controversial bills until issues raised about them were resolved.