One boat went down off the coast of the small Greek islet of Kalolimnos, killing 34 people, including 11 children.
Another eight people died after a boat sank off the island of Farmakonisi.
Over a million migrants arrived in Europe last year. More than 700 died in the Aegean crossing from Turkey to Greece.
German Chancellor Angela Merkel is on Friday meeting Turkish Prime Minister Ahmet Davutoglu in Berlin to discuss the crisis.
Cabinet ministers from both countries will be in attendance.
On Thursday, French Prime Minister Manuel Valls warned that Europe’s migration crisis was putting the EU at grave risk.
Mr Valls told the BBC that Europe could not take all the refugees fleeing wars in Iraq or Syria. If it did, he said, it could “destabilise our societies”.
The Greek coastguard said it had rescued 26 people from the sinking of the wooden sailboat off Kalolimnos, but that it had recovered 34 bodies – 16 women, 11 children and seven men.
It was not known how many were on the boat and a search is continuing for more survivors.
The boat off Farmakonisi was carrying 48 people. Forty made it to shore and one girl was rescued, but the bodies of six children and one woman were found.
Source BBC