"Any discussion about the future of Ukraine must include the legitimate government of Ukraine," the president said.
Instead, the Crimean Provincial Parliament voted to split from Ukraine and join Russia.
Crimeans will hold a referendum in ten days.
Russian lawmakers in Moscow welcomed the move, which Russia's troops are in position to enforce.
To punish Russia, President Obama ordered sanctions and visa bans on unnamed individuals supporting the apparent grab of Crimea.
"These decisions continue our efforts to impose a cost on Russia," he warned.
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