If the missing are confirmed dead, it will be the deadliest sea crossing in that part of the Mediterranean so far this year.
A spokeswoman for the Spanish coastguards told AFP that ‘we suppose’ the migrants have drowned.
She added that crews were still searching for potential survivors in the seas near Alboran Island.
The rubber boat was discovered some 50km southwest of the island, which lies in the westernmost point of the Mediterranean.
The surviving men, all under the age of 25 and from sub-Sahara Africa, said there were more than 50 people on the boat, which had drifted for several days after leaving Morocco.
They were taken to hospital in Almeria.
Some 60 migrants have died so far this year trying to reach Spain.
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