Flores, who pitched with the Class A Lake County Captains in the Midwest League last year, now must remain with the Mariners for the entire 2011 season or be offered back to the Indians for $25,000.
"He's an upside guy with a nice arm," Mariners general manager Jack Zduriencik said, noting Flores threw against the Mariners' Clinton farm club in the playoffs last season and was seen twice by scouting director Tom McNamara.
The Venezuelan-born reliever was 1-1 with six saves and a 2.14 ERA in 42 innings last year for Lake County, striking out 51 while walking just seven. He held opponents to a .224 batting average.
Flores originally signed with the Indians as an undrafted free agent in 2005. He posted a 3.92 ERA with 129 strikeouts in 156 innings in four seasons in Cleveland's system.
"He has limited innings, so you sit and evaluate on taking a guy like this," Zdurienick said. "But we talked to our people in Venezuela and they had nice things to say. You look at the list that's available and see a guy that's young with a good arm, throws strikes and has an upside, so we'll see what happens."
A year ago, the Mariners picked up reliever Kanekoa Texeira from the Yankees in the Rule 5 Draft and he made the team out of Spring Training, but was designated for assignment after two months with Seattle and wound up getting claimed off waivers by Kansas City.
Texeira was a 23-year-old who'd been pitching Double-A ball when selected. Zdurienick acknowledged it's uncommon for a Class A prospect to attempt the jump to the big leagues.
"It's unusual if he sticks," Zduriencik said. "But again, the key thing is he's a strike-thrower, has good size and [a power] arm, so we'll see what happens. When you take a kid that's young and has to make this kind of leap, it's a great challenge to any player. But it's technically a $25,000 gamble."
The selection puts the Mariners' 40-man roster at a full 40, so someone will have to be moved to create space for the expected signing of free-agent designated hitter Jack Cust once he passes a physical and his agreement is made official.
The Mariners didn't lose anyone in the Major League portion of the Rule 5, but did have outfielder Jose Rivero selected off their Double-A Jackson roster in the Minor League Rule 5 Draft. Rivero split the 2010 season between Class A Everett and Advanced Rookie League Pulaski.
Rivero, a 20-year-old from Venezuela, hit .295 with seven home runs and 35 RBIs in 190 at-bats for Pulaski and .189 with no home runs and six RBIs in 53 at-bats with Everett.