The Greek harbour police did not give the victims' ages or nationalities and it was not clear if the two were related.
According to testimony from the survivors, 49 people were on board the dinghy when it capsized in the Aegean Sea off the northern coast of Lesbos.
Read: Migrant boat heading to Greece from Turkey sinks, 13 dead
Twenty-year-old Nilofa Ghonami, an Iranian-born Afghan woman, told AFP that the boat they were sailing in -- which was only supposed to hold 14 people -- had broken in half.
"There was water (in) the boat and all the people stand up in one group and the middle of the boat broke and all the people went to the sea," the survivor said.
"Turkish police saw us and didn't help us, a second boat coming from Turkey to Greece saw us and (called) the Greek police who helped us," she said.
"We were two hours in the sea, it was very hard," said Ghonami, who was studying to become an engineer in Iran
"In Iran, we are just living, we are not alive. I want to improve my level of living," she said.
The island of Lesbos has become one of the main points of entry to the EU for thousands of migrants from the Middle East and Asia arriving from Turkey which lies just eight nautical miles away.
Read: Four children missing after migrants' boat capsizes off Greece
Some 515,000 people have reached Europe via the Mediterranean this year, figures from the UN refugee agency UNHCR show, many of them undertaking perilous journeys in inflatable dinghies.
Nearly 3,000 others have died or disappeared during the crossing, the UNHCR said earlier this week.
More than half of those entering Europe are fleeing the conflict in Syria.
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