The Eugene Emeralds had been affiliated with the Padres since 2001. The Cubs were affiliated with the Northwest League's Boise Hawks from 2001-14.
"We are looking forward to working with [general manager] Allan Benavides and the entire Emeralds organization, and are eager to begin working with the local community," said Jason McLeod, the Cubs' senior vice president of scouting and player development. "The Eugene ballclub offers a first-class facility at the University of Oregon, one of the most impressive facilities in short-season baseball."
The Emeralds, who began play as an independent team in the inaugural Northwest League in 1955, have partnered with nine Major League organizations in their 60-year history, winning three Northwest League championships and moving into their current ballpark, PK Park, in 2010.
"The Emeralds could not be happier to announce this new partnership with the Cubs," Benavides said in a statement. "We are excited to introduce a new brand of baseball at PK Park and look forward to a long-lasting relationship as the Cubs' Northwest League affiliate."
Adam Berry is a reporter for MLB.com. Follow him on Twitter at @adamdberry. This story was not subject to the approval of Major League Baseball or its clubs.