Lynch and Bowlen developed a friendship following the former NFL safety's playing days, and he saw the Broncos owner as a mentor.
Lynch, a member of the Broncos' Ring of Fame, posted the following via Twitter following the word of Bowlen's passing.
"Denver was one of those kind of iconic franchises where you knew the reputation around the league — and it was earned — was that they did things right," Lynch said on NFL Network.
Lynch believed Bowlen set a standard for NFL success and cared deeply not only about winning, but his players too.
"We're very fortunate to have ownership in San Francisco that embodies a lot of those qualities," Lynch said. "To me, Mr. B was so great as an owner because he was always present. He was there all the time, but he very much believed in hiring good people and allowing them to do their work. You always knew that the resource of his support was going to be there, but he let people do their work."
Bowlen was part of the Broncos' trio of Super Bowl championships. Although, his deteriorating health prevented him from attending their latest victory in Super Bowl 50 and had gave up control of the Broncos in July of 2014. He was selected to the Pro Football Hall of Fame earlier this year.
"There's owners that are great owners," Lynch continued. "Then there's owners that kind of transcend that and have really helped shape this league. Pat Bowlen, although he did it often times kind of in the background, was very influential in this league; the TV deals, all those things. You talk to people who have been around for a while, his imprint is all over this league."
The 49ers issued their own statement following the passing of Bowlen.
"His legacy will run deep in this league's history," Lynch added.
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