The court ruled today that with fewer than 50,000 members and representation in fewer than half of Russia's regions, the Republican Party was too small to be considered a party under a 2004 Russian law.
Court officials said Russia's Federal Registration Service filed the case against the Republican Party.
"This is direct persecution of the opposition," Republican Party co-Chairman Vladimir Ryzhkov told RFE/RL after the decision. "There has been systematic persecution of the Republican Party across the whole country ever since I and several other politicians joined the Republican Party exactly two years ago."
Ryzhkov said the party has 58,000 members and is represented in the majority of Russia's regions. He called the Federal Registration Service's method of counting party members "dubious" because it excluded people who could not be reached by telephone.
"The court accepted absolutely raw, worthless pieces of paper presented by the Registration Service and took for granted its claim that [the Republican Party] had 42,000 members, as registered by the Registration Service, as opposed to 58,000 members actually registered with us," Ryzhkov said.
"We strongly disagree and we have already stated that we will appeal this decision to the Collegium of the Supreme Court," he added.
Ryzhkov said if the party did not find relief in the Russian courts it would appeal to the European Court of Human Rights in Strasbourg.
In recent years, Ryzhkov has emerged as one of President Vladimir Putin's most ardent critics.
Ryzhkov was a leading member of the pro-Kremlin party Our Home Is Russia in the 1990s before becoming an independent. He became co-chairman of the Republican Party in 2005.
A Long Tradition
The Republican Party is one of Russia's oldest opposition parties. It was formed by liberal defectors from the Soviet Communist Party in 1990 during Mikhail Gorbachev's perestroika-era reforms.
Also today, prosecutors asked the Moscow Municipal Court to ban the National Bolshevik Party. Prosecutors ordered the party's activities suspended pending a ruling. The party's leaders called decision politically motivated.
Led by the iconoclastic novelist Eduard Limonov, National Bolshevik Party says it strives for social justice, but also promotes nationalist ideas.
The party's members wear hammer-and-sickle armbands and are renowned for political pranks that lampoon President Vladimir Putin and the Kremlin leadership.
(with material from agency reports)