MEPs "call on Russia to release without further delay all illegally and arbitrarily detained Ukrainian citizens, both in Russia and in the temporarily occupied territories of Ukraine," a resolution said.
The strongly worded resolution, overwhelmingly approved by MEPs, marked the three-year anniversary of Moscow's March 2014 takeover of the strategic Black Sea peninsula.
The document expressed "concern over the many credible reports of cases of disappearances, torture, and systemic intimidation of local citizens opposed to the annexation of Crimea".
The lawmakers meeting in Strasbourg, France said Crimea's Tatar minority and heritage "seem to be prime targets for repressions".
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The measure comes after EU governments on Monday prolonged by another six months sanctions against Russian and Ukrainian individuals over their role in the Ukraine crisis.
Another set of sanctions specifically linked to Russia's annexation of Crimea, were rolled over for a year in June 2016.
The EU has imposed a whole series of punitive measures over Ukraine where the Minsk ceasefire accords brokered by France and Germany with Kiev, Moscow and the rebels repeatedly fail to hold.