The San Francisco 49ers have been one of the most successful teams in the NFL over the last three seasons with head coach Kyle Shanahan calling the shots. 

Since 2021, the 49ers have gone 35-16, won the NFC West twice, reached the NFC championship game three straight years and played in the Super Bowl. 

And they don’t have a championship to show for it. 

The 49ers lost to Patrick Mahomes and the Kansas City Chiefs in this year’s Super Bowl, the second time Shanahan and the Niners have fallen to the Chiefs in the final game of the NFL season. 

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San Francisco has been unable to get over the hump, putting Shanahan in the conversation with coaches who have failed to win the big one. 

In the days following San Francisco’s overtime loss in the Super Bowl, there were major changes to the 49ers coaching staff.

Let’s look at the moves. 

49ers move on from defensive coordinator Steve Wilks

After just one season, Steve Wilks is out as defensive coordinator in San Francisco. 

Shanahan announced Wednesday Wilks had been relieved of his duties and that the search for a new defensive coordinator would include internal and external candidates. 

“(It was a) really tough decision because it really says nothing about Steve as a man or as a football coach,” Shanahan said. “He’s exactly what we wanted as a man. He’s a great football coach. But where we’re going and where we’re at with our team, from a scheme standpoint, looking through it all throughout the year to these last few days, we felt pretty strongly that this was a decision that was best for our organization.

“Even though it was one I didn’t want to make, it was something that I realized that I think a different direction is what’s best for the organization.”

Steve Wilks vs Rams

Wilks was hired last offseason to replace DeMeco Ryans, who took the head coaching job with the Houston Texans

Under Wilks, the 49ers’ defense had an up-and-down season and took small steps back after a stellar 2022 season. 

San Francisco went from allowing the fewest points in the NFL (16.3) to allowing 17.5 (third in the NFL) per game in 2023. 

Against the Detroit Lions in the NFC championship game, San Francisco fell behind by 17 points in the first half. In the days following the win, Wilks was critical of his unit’s effort. 

“Collectively as a team, I can tell you as a defense it’s unacceptable,” Wilks said. “All right. We talked about that. I wish I could tell these guys on play four, on play 27, this is what’s going to happen. You don’t know. 

“So, we’ve got to make sure that we play every down as if it’s going to be the difference in the ball game. And you could see on those particular plays, it wasn’t to our standard. Those guys understand and know that and, quite honestly, it was embarrassing.”

Assistant head coach/running backs coach Anthony Lynn leaves for Commanders

After two seasons, Anthony Lynn departs San Francisco for the Washington Commanders, where he will be the run game coordinator under Dan Quinn. 

In 2023, San Francisco’s rushing attack was ranked third in yards per game (140.5), and Christian McCaffrey led the league in rushing with 1,459 yards. 

Anthony Lynn coaches against Seattle

In Lynn’s first season, the Niners were eighth in the NFL with 138.8 rushing yards per game. 

Pass game coordinator Klint Kubiak takes coordinator job with Saints

The 49ers lost another member of its offensive staff when Klint Kubiak was named the offensive coordinator of the New Orleans Saints Wednesday. 

A 14-year coaching veteran, Kubiak spent one season in San Francisco. 

“We are excited to announce Klint Kubiak as our offensive coordinator,” Saints head coach Dennis Allen said in a statement. “I want to thank the various impressive candidates that we interviewed throughout this process. 

“Klint has done an excellent job in a variety of roles in 10 years in the NFL and has valuable play-calling experience. He has played an important role in the growth of many players throughout his career, starting with the quarterback position. 

Klint Kubiak coaches the Niners

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“I look forward to us getting to work as we form our offensive staff and to see Klint lead that group, play a pivotal role in the development of our players on offense and maximize our strengths on offense.”

The 49ers’ offense was second in the NFL in yards and third in points per game in 2023. San Francisco’s passing attack ranked fourth in the league with 257.9 yards per game. 

James Cregg takes Las Vegas Raiders’ offensive line job

James Cregg, who spent the last two seasons with the 49ers as an assistant offensive line coach, will be the offensive line coach in Las Vegas, according to NFL Network.

Cregg will now work with Antonio Pierce, who will be in his first full season as head coach of the Raiders. 

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Pierce became interim head coach in Las Vegas during Week 9 after owner Mark Davis fired Josh McDaniels in just his second season. 

Darryl Tapp joins Lynn in Washington

Tapp will be with Lynn in Washington as he becomes the next defensive line coach of the Commanders. 

Tapp spent three years with the Niners as an assistant defensive line coach.

San Francisco finished eighth in yards allowed per game in 2023 (308.9).

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