Police said they found the bodies of Alvarado, 19, and her sister Sofia Trinidad, on a river bank, after mounting an exhaustive search.
“We are 100 percent sure that it’s them,” police chief Leando Osorio said.
The two women disappeared Thursday near Honduras’ northern city of Santa Barbara after attending a birthday party at a local resort.
Officials on Tuesday arrested a boyfriend of Trinidad’s, Plutarco Antonio Ruiz, as a central suspect.
Alvarado had been set to fly to London on Wednesday for Miss World.