McDonald's said in a statement posted on its Ukrainian website that the decision was taken "for manufacturing reasons beyond the company's control".
But it also reflects a broader uncertainty among major Western companies about their future positions in Russia following the Kremlin's military intervention in Ukraine.
Washington and the European Union have both imposed targeted punitive measures against Moscow officials and threatened broader economic sanctions that could affect the operations of McDonald's and other companies with a broader Russian presence.
It also promised its Crimean employees jobs at its Ukrainian stores and to relocate their family members to the mainland at its own expense.
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The US chain's announcement was cheered by some prominent Russian politicians who have been waging an increasingly vitriolic war of words with the West since last month's start of the Crimean campaign.
"It's very good that McDonald's is closing its branches in Crimea. Let them close their branches over here too," said nationalist Russian lawmaker and former presidential contender Vladimir Zhirinovsky.