Hennadiy Trukhanov, 60, said he would take his case to court, denying having a Russian passport and insisting that he remained mayor.
Ukrainian officials are prohibited from holding dual citizenship.
"The Russian citizenship of several individuals has also been confirmed, and corresponding decisions have been prepared. The decree has been signed," Zelenskiy said on Telegram after a meeting with intelligence chief Vasyl Malyuk, without naming names.
In his evening address, Zelenskiy said that he would appoint someone soon to head up a new military administration to run the city, making clear he was moving to have Trukhanov replaced.
"Too many security issues in Odesa have remained unresolved for too long," he said.
Trukhanov could now face deportation.
The remarks echoed his comments from last week in which he accused Odesa's "local leaders" of failing to do enough to protect residents from flooding last month that killed 10 people.
The SBU domestic security agency said in a statement that it had evidence Trukhanov had a valid Russian passport.
It posted a picture on Telegram appearing to show a photocopied Russian passport page bearing Trukhanov's name and face.
Trukhanov said in a video address: "I will appeal the decision to strip me of my Ukrainian citizenship in the Supreme Court. And, if that is not enough, I will appeal to the European Court of Human Rights."
A source familiar with the matter said Zelenskiy had also revoked the citizenship of two other people.
Under Ukraine's constitution, the president has the power to strip people of their citizenship.
By creating a military administration in charge of the city, Zelenskiy would obtain more direct control over it.
The president handpicks the heads of military administrations.
Russian forces were unable to reach the city of Odesa in their rapid offensive push across southern Ukraine in February 2022 but Odesa has since been battered by regular Russian missile and drone strikes throughout the war.
Trukhanov has spoken out against the Ukrainian movement of "de-Russification" that began in 2014 when Russia seized and annexed the Crimea peninsula and which has accelerated since its full-scale invasion.
He opposed the dismantling of Odesa's statue to Russia's Catherine the Great who founded the port in 1794 and another to Alexander Pushkin, the Russian playwright.
Taking such a stance has made him a divisive figure.
A crowd of dozens gathered in Odesa to demand his replacement late on Tuesday.
Oleksiy Honcharenko, an opposition MP from Odesa and a fierce critic of Zelenskiy, said Trukhanov had "many questions" to answer but nevertheless condemned the stripping of his citizenship.
"Today they will take Trukhanov away and we will all rejoice because he is bad but tomorrow this machine of repression will be unleashed against inconvenient people," he wrote on Telegram.
with DPA
