The 49ers fire defensive coordinator Steve Wilks after their Super Bowl loss

SANTA CLARA, Calif. — The San Francisco 49ers fired defensive coordinator Steve Wilks on Wednesday, three days after losing the Super Bowl to the Kansas City Chiefs.

Coach Kyle Shanahan announced the decision to move on after one season with Wilks in charge of the defense. Shanahan called it a “really tough decision” but said he wants to find a coordinator who was a better scheme fit for the talent on San Francisco’s defense.

“We felt pretty strongly that this was the decision that was best for our organization,” he said. “Even though it was one I didn’t want to make, it was something that once I realized that a different direction was what’s best for our organization, it’s something that I have to do.”

Shanahan hired Wilks after losing DeMeco Ryans, who was hired as head coach in Houston after helping San Francisco field the top defense in the league in 2022.

Shanahan wanted to keep the same system that had been successful, and Wilks had the difficult task of trying to add his own wrinkles to an unfamiliar scheme.

“That was the hardest part. I knew that was a challenge,” Shanahan said. “We have committed to not just a system, but the players that have been in the system from our D-line, our linebackers, they played in it for such a long time. It was my goal to not have to change all of them and bring in Steve who was unbelievable and how loyal he was and him trying to do it.

“But it just ended up not being the right fit. It hurt for me to do this, but that’s exactly why I had to.”

The results were mixed during the regular season. Wilks was forced to move from the booth to the field following a three-game losing streak in October, and San Francisco’s production on defense dropped marginally in the regular season.

But issues came up in the playoffs, with the run defense getting gashed by Green Bay and Detroit in the first two playoff games, when coaches and players questioned the effort given. The Niners then came up short defensively down the stretch against Patrick Mahomes and the Chiefs.

After holding Kansas City to six points on the first nine possessions in the Super Bowl, the Niners allowed two touchdowns and two field goals on the final four drives to lose 25-22 in overtime.

Defensive end Nick Bosa said after the game that the team was unprepared for Mahomes to keep the ball on key runs that led to first downs on the game-winning drive.

The Niners were the first team to fire an offensive or defensive coordinator after losing the Super Bowl since Atlanta fired defensive coordinator Richard Smith after blowing a 28-3 lead to New England in Super Bowl 51. Shanahan was the offensive coordinator for the Falcons in that game and left to take over San Francisco following the loss.

Wilks’ background was in the secondary after the previous two coordinators in San Francisco had been linebackers coaches, and Shanahan said the Niners struggled to tie together the secondary with the front seven this season.

Shanahan said he will look at internal and external candidates to find a replacement. He said he is willing to consider a coordinator who will bring in a new system but believes the current system is probably best for the roster he has.

“When you have a group of guys who have played at a high level doing certain things a specific way for a while, I do feel that’s the best thing to do for them,” he said. “But if I find something that I believe in, that I can be sold on that could be a better avenue, I would never hesitate to do that.”

The Niners will have several other coaching changes on their staff, with at least four coaches getting hired away by other teams.

Passing game coordinator Klint Kubiak will become offensive coordinator in New Orleans, running backs coach Anthony Lynn will be run game coordinator in Washington, assistant defensive line coach Darryl Tapp will take over as defensive line coach in Washington and assistant offensive line coach James Cregg will become offensive line coach in Las Vegas.