Zemtsov has been charged with blackmail, after allegedly demanding a monthly payment of $30,000 for withholding compromising information about acting Agriculture Minister Alexei Gordeyev.
If found guilty, the deputy editor faces 7-15 years imprisonment.
Nezavisimaya Gazeta, a highbrow daily, has a print run of around 50,000 copies per issue and the paper's website has about 70,000 daily visitors.
The paper was owned by the exiled oligarch, Boris Berezovsky, a fierce critic of the Kremlin, until 2005, when it was bought by the former State Duma lawmaker Konstantin Remchukov.
While it often criticizes Kremlin policies, Nezavisimaya Gazeta, whose name translates as the Independent Newspaper, is not a recognized opposition newspaper.
Nezavisimaya Gazeta called the arrest of Zemstov "a carefully planned provocation".
