The All-Pro linebacker missed last season's second meeting with the division-rival Seattle Seahawks, sidelined for three games with an injured right hamstring.
And San Francisco's run of holding rushers below 100 yards ended when Lynch went for 107 in the 49ers' 19-17 win at Seattle on Dec. 24. Now, the Seahawks star comes to Candlestick Park for Thursday night's prime time NFC West showdown with a healthy Willis waiting on the other side of the ball.
"He runs the ball hard, a very elusive guy," Willis said earlier this week "He's a very hard tackle. We're going to have to have everybody swarming to the ball and not expecting one guy to make the play. He's by far one of the best running backs in the league and will be one of the best backs we face all year long. We've got to face him twice."
And the Niners, tied with Seattle and Arizona for first place at 4-2, will be looking to bounce back from Sunday's embarrassing 26-3 home defeat to the defending Super Bowl champion Giants.
Slowing down Lynch will be a top priority if the Niners are going to win this one. He ranks first in the NFC and third in the NFL with 549 yards on 128 carries.
"Their running game is the bread and butter of their offense," defensive coordinator Vic Fangio said Tuesday. "And everything works off of that. He's one of the best backs in the league. He's the best back we played last year by far. He broke more tackles than any back we played against last year. He broke the most against us."
Willis was held out of the regular season finale in 2010 for the first missed start of his career since San Francisco selected him with the 11th overall pick in 2007 out of Mississippi—that time because of a broken bone in his hand. Then, going down again late last season for the NFC West champions was even harder for him. The 49ers went 13-3 and earned a first-round bye in the playoffs.
"It was very tough. I'm a very competitive guy and I love being out there on the field any chance I get," Willis said. "Sometimes you may take things for granted, but when you don't get to do the things you love to do, it stings a little bit. I feel good. We feel good. We know Thursday's a big game for us. One, because it's the next game but also it's a game in our division. We want to start it off right."
San Francisco's streak of 36 straight games without a 100-yard rusher dated to Ryan Grant's 129-yard day for Green Bay on Nov. 22, 2009.
Not only did Lynch end that mark in December, his 4-yard touchdown run in the fourth quarter was the first TD rushing allowed by San Francisco all season.
Lynch also will have something to prove Thursday night. His 41 yards on 15 carries in Seattle's 24-23 comeback victory against the Patriots on Sunday were his fewest since Week 8 of last season, when he was held to 24 yards by Cincinnati.
New York's Ahmad Bradshaw gained 116 yards and ran for a 1-yard score Sunday against San Francisco. Lynch has a knack for breaking tackles, so Fangio has his unit focusing on fundamentals this week.
"We've got to play a little bit more physical in the front seven. We've got to get off blocks better. We've got to tackle better," Fangio said. "In the fourth quarter last week, we didn't get that done."
NOTES: 49ers LT Joe Staley said he expects to find out Wednesday whether he will play Thursday. He suffered a concussion during the loss to the Giants. He feels ready to play but knows the decision isn't his to make. "It wasn't that serious," Staley said. "We're going through the process right now. We have to go through different stages. We met with the neurologists yesterday. Everything went well there and today we have a workout. We'll go out on the field and see how everything goes with that." If Staley can't go, Alex Boone would move over from right guard to replace him and Leonard Davis would start at RG. ... San Francisco will make a bid for the 2016 Super Bowl in its under-construction new stadium next to team headquarters that is set to open for the 2014 49ers season. "We are excited to bid for the first Super Bowl in the Bay Area since January of 1985," CEO Jed York said. "Nothing brings a region together like a Super Bowl. Now we have to work together to show the new stadium in Santa Clara will put on a great show."