Although the cause of death hasn't been determined, New Castle County Police Cpl. John Weglarz said investigators don't suspect foul play.
Weglarz said search teams found the bodies of Christopher Valentine, 25, of Hockessin, and his friend Jean Baptista, 25, of Clark, N.J., on Monday afternoon, one day after Valentine's mother reported him missing.
Gov. Jack Markell offered his condolences to the men's families and friends.
"While we had certainly prayed that our state would get through Hurricane Irene without the loss of life, we unfortunately now know that that's not the case," Markell told The Associated Press in a telephone interview.
The two men had been at a friend's house Saturday night as the Category 1 hurricane rumbled up the East Coast. They left shortly before midnight to head out on foot through the driving rain and gale-force winds to Valentine's house about two miles away, Weglarz said.
"They were walking during the height of the storm," he said.
The men texted friends that they were running through the hurricane, according to police.
Search teams found their bodies in Mill Creek Branch, a waterway between the friend's house and Valentine's house, Weglarz said.
The Wilmington area was drenched with about 6 inches of rain that night, causing widespread flooding and flash floods.
Weglarz said their friends told police the men had been drinking.
Hockessin is an inland community of nearly 14,000 people about 10 miles northwest of Wilmington.
