The Twins are looking for a new top farm team, and the St. Paul Saints are front and center in the discussion.

The Twins officially informed the owner of the Rochester Red Wings that the New York site will no longer be their Class AAA affiliate. It’s a move that is part of a massive overhaul of minor league baseball.

Red Wings President/CEO and COO Naomi Silver, on the team’s website, said Twins President Dave St. Peter “stressed the deep appreciation the Twins have had for our relationship, and gratitude for our partnership. We will always have fond memories of our time spent as a Twins affiliate.”

As part of a complete restructuring of the relationship between MLB and minor league baseball, under negotiation all summer and expected to be finalized later this month, major league affiliates will be reduced to 120 teams — four per MLB parent plus a training-complex team for rookies — with short-season leagues being eliminated. Major league teams are using the reorganization to line up more geographically friendly affiliates.

Current Twins, MLB minor-league affiliates

“The Twins will not be commenting on our affiliates for 2021 at this time,” St. Peter said.

The 2020 season was to be the Twins’ 18th year with Rochester, but the COVID-19 outbreak forced teams to develop a select number of minor league players at alternate training sites during the 60-game regular season.

The Twins trained their minor leaguers at CHS Field in St. Paul, and just might continue the relationship. The Saints, who play in the independent American Association, have been talking with the Twins and MLB about an affiliation in recent months and, according to a source with knowledge of those discussions, those talks have been progressing well. In fact, there is a belief that a framework of a deal is in place.

One big hangup: The Saints would have to write an eight-figure check — perhaps as much as $20 million — in order to become an affiliate. There are no indications that their ownership group, which includes Marv Goldklang, Mike Veeck and comedian/actor Bill Murray, is willing to do that. The Saints have been seeking better terms as talks have continued, with some positive signs.

The $20 million, which would be paid to Minor League Baseball, is based on the valuation of a Class AAA franchise. As the minors are reorganized, some teams will be reclassified. Those moving up a level or two will have to pay. Those moving down will receive money. In the end, it’s supposed to balance. Since the Saints would be coming in from independent ball, they would have to pay the most, although the Twins could pitch in.

The Twins began the process looking at a few options, with Wichita and Sioux Falls, S.D., among the possibilities. A requirement that Class AAA teams have stadiums with a capacity of at least 10,000 would be waived in St. Paul’s case; the Saints had a top-10 attendance across all of minor league baseball in 2019 at CHS Field, which has a capacity of 7,200.

The Saints, Sugar Land (Texas) Skeeters and Somerset (N.J.) Patriots are believed to be the only three teams from independent baseball that will become affiliates.

More details will be revealed by the end of the month now that the MLB season is complete and the league can turn its full attention to reshaping minor league baseball. Among the plans are mandatory 10-year agreements with each affiliate and the possibility of the Class A Florida State league — currently a high-A league — becoming a low-A league while an organization like the Midwest League moves from low-A to high-A.

There also is a Baseball Digest report that Class AA Pensacola, currently a Twins affiliate, will become a Marlins affiliate. There were no indications Tuesday whether the Twins had informed the Blue Wahoos of their intentions.