They considered a US plan for a halt to Russia's military build-up on the border with Ukraine, a troop withdrawal in Crimea, and moves to protect the Russian speakers in the region.
Mr Putin stressed the threat posed by "extremists" in Kiev, the Kremlin said.
Russia's annexation of Crimea has sparked international condemnation.
In the hour-long phone call, the US president urged Mr Putin to avoid the build-up of forces on the Russian border.
"President Obama underscored to President Putin that the United States continues to support a diplomatic path... with the aim of de-escalation of the crisis," the White House said in a statement.
"President Obama made clear that this remains possible only if Russia pulls back its troops and does not take any steps to further violate Ukraine's territorial integrity and sovereignty."
The two leaders agreed that their foreign ministers would meet soon to discuss the next steps.
Source: BBC News
Tags:Relationships
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