The 24-year-old, who played 33 times for Switzerland and was captain of Young Boys Bern's women's team, had gone missing on Saturday.
"The Swiss Football Federation (SFV) has the painful task of informing about the death of its national player Florijana Ismaili. We are all upset, deeply affected and very, very sad," said an SFV statement.
The SFV said that Ismaili had jumped into the water from a rented boat and never resurfaced. The body was found on Tuesday after searches by the Italian authorities, it said.
"The SFV expresses its sincere condolences to the family, relatives and friends of Florijana Ismaili and wishes everyone all the strength in this difficult time."
FIFA president Gianni Infantino said in a statement that it was an "extremely sad moment for all the football community, particularly at a time when we gather at the FIFA Women’s World Cup."
Switzerland and Liverpool forward Xherdan Shaqiri was among those to send condolences.
"I am deeply shocked by the death of Florijana Ismaili," he said on Twitter. "My family and I would like to express our condolences to the Ismaili family and the near ones."
(Writing by Brian Homewood; Editing by Ian Ransom)
