Goals by Kroos in the seventh minute and Mueller in the 21st built a 2-0 lead. After Lukas Podolski scored for Arsenal in the 55th, Mario Mandzukic got Bayern’s final goal in the 77th.

The second leg of the total-goals series is in Germany on March 13.

“Let’s not hide the truth,” Arsenal manager Arsene Wenger said, “it will be very difficult. We will try to make the impossible possible.”

In Tuesday’s other game, Joao Moutinho scored in the 56th minute to give Porto a 1-0 win over visiting Malaga.

The first leg ends Wednesday when AC Milan hosts Barcelona and Schalke is at Galatasaray.

While Bayern leads the Bundesliga by 15 points and reached the Champions League final in two of the last three years — losing both — Arsenal is in the midst of the most trying season since Wenger was hired in October 1996.

Arsenal is fifth in the Premier League, 21 points behind first-place Manchester United and four back of rival Tottenham for England’s last berth in next season’s Champions League.

The Gunners, who haven’t won a trophy since the 2005 FA Cup, were knocked out by fourth-tier Bradford in December’s League Cup quarterfinals and were eliminated from the FA Cup’s fifth round by second-tier Blackburn last season.

Now this year’s Champions League title is a longshot.

“You have to give credit for their class,” Wenger said of Bayern. “In patches in the first half, there was a difference in quality.”

Arsenal central defenders Per Mertesacker and Laurent Koscielny had a poor night, with the first goal coming after Bayern collected an errant clearance from Koscielny. Mueller crossed for Kroos, who beat goalkeeper Wojciech Szczesny with an 18-yard volley.

Mueller scored when he poked the ball into an unguarded net after Szczesny parried a header from an unmarked Daniel Van Buyten.

Arsenal’s players were jeered when they walked off at halftime, while Bayern fans sang another rendition of “Football’s Coming Home” in English.

“We didn’t start great and that’s been a thing for us this season,” Arsenal midfielder Jack Wilshere said. “Maybe it’s a bit of nerves or anxiety because we show what we can do when we play.”

Podolski cut the gap when he headed Jack Wilshere’s corner kick into an open net. But Mandzukic finished a sweeping move by bundling in Philipp Lahm’s low cross at the far post, the ball looping up off the Croatian’s heel and beyond Szczesny.

“We are currently in astonishing form,” said Bayern coach Jupp Heynckes, who will be replaced by Pep Guardiola this summer. “Our quality is we can punish even the smallest mistakes of our opponents.”

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The Gunners face Bayern Munich in the Champions League on Tuesday night and manager Arsene Wenger had made several changes, with Jack Wilshere, Theo Walcott and Santi Cazorla all starting on the bench.

Even so, there should still have been enough quality to see off the lower-division Championship side.

Gervinho missed a great chance at the end of the first half that proved costly as Colin Kazim-Richards’ scrappy effort after 72 minutes proved enough to inflict Arsenal’s first home FA Cup defeat since their move to the Emirates Stadium and hand Rovers a memorable win.

Wenger offered no excuses for the loss.

“We had 11 international players on the pitch at the start of the game. We had a lot of the ball and [Blackburn] defended well. We had 16 shots at goal, they only had one shot at goal,” he said. “We made a massive mistake on the goal and we were not good enough to win the game, it is as simple as that.

“Not one defeat is acceptable. You are in this job to win every single game.”

Arsenal now faces the possibility of an eighth season without silverware, unless it can come through in the Champions League. The home fans vented their frustrations as boos rang out around the Emirates at the final whistle.

“You do not want your fans to be happy when you lose at home to Blackburn when the team has one shot at goal,” Wenger said. “It is very painful and very disappointing to lose a game like that. What is important now is to focus on the next one.”

Blackburn, which still has not conceded a goal in this season’s FA Cup, fashioned an early chance when a free kick from the left was flashed through the Arsenal six-yard box and Markus Olsson knocked the loose ball wide at the far post.

Alex Oxlade-Chamberlain had been given a chance to impress in midfield for Arsenal, and the England international was soon on the ball, releasing Tomas Rosicky down the right only for the Czech winger to clip his attempted cross behind.

Oxlade-Chamberlain then decided to do it himself, charging into the Blackburn penalty area and cutting a pass back across the six-yard box where Bradley Orr hacked clear.

The Rovers full back was shown a yellow card by referee Mike Dean in the 12th minute after scything down Gervinho as the Ivory Coast forward, back from the African Nations Cup, looked to break down the left.

Arsenal fans behind the goal at the Clock End called for a penalty when Rosicky’s cross hit Scott Dann on the arm as he blocked it behind for a corner, but the referee was not interested.

The home side continued to press, forcing a succession of corners.

In the 25th minute, Arsenal finally got the delivery right from Rosicky, and Abou Diaby rose to power a bullet header goalward, which Rovers goalkeeper Jake Kean beat away at full stretch with a magnificent reaction save.

Kean was on hand to palm away a looping header from captain Thomas Vermaelen, fit again following an ankle problem, as the Rovers goal was under siege again.

The best opening came just before halftime when Rosicky slipped Gervinho into the penalty area, but despite holding off the defender, the Ivory Coast forward dragged his shot wide of the post — before dropping to his knees and looking to the heavens.

Blackburn started the second half brightly.

Vermaelen had to be alert as he touched a cross behind with Jordan Rhodes waiting to knock the ball in at the far post.

Arsenal slowly regained momentum, and Diaby flashed a 25-yard effort wide.

Blackburn made a change after 63 minutes when Markus Olsson was replaced by former Arsenal man David Bentley, who rejoined his old club Rovers on loan from Tottenham — and received a less-than-warm welcome from the home support.

Rosicky crashed a 20-yard effort off the crossbar and Rovers defender Grant Hanley made an important block as Gervinho cut in from the right.

With 20 minutes left, Wenger had seen enough and made a triple substitution as Walcott, Wilshere and Cazorla replaced Gervinho, Rosicky and Oxlade-Chamberlain.

However, out of nothing, Blackburn snatched the lead.

Martin Olsson burst into the left side of the penalty area and drilled the ball, which Wojciech Szczesny parried into the path of Kazim-Richards, whose scuffed follow-up effort bounced onto the post and in.

Arsenal immediately went on the offensive, with Walcott surging down the right, but was faced with a wall of blue shirts.

Diaby’s effort was charged down and Kean somehow saved a close-range header from Walcott before Giroud’s effort in stoppage-time was blocked as Rovers clung on for a famous win.

“To come to Arsenal and get through a cup tie is one thing, but to keep a clean sheet and defend as well as we did is another, and that is testament to our players,” said Blackburn boss Michael Appleton. “We have two man-mountains in the centre of defense.”

Later Saturday, a stoppage-time goal from substitute Matt Smith earned Oldham a 2-2 draw against Everton and a replay at Goodison Park.

Jordan Obita gave the Latics a 14th-minute lead at Boundary Park, smashing home with his left foot.

Victor Anichebe then leveled 11 minutes later with a crisp strike into the bottom left corner, and Phil Jagielka’s header three minutes after the interval looked to have done enough to give Everton the win.

However, Smith came out on top in a penalty-area scramble to head in an equalizer in the fourth minute of stoppage time.

Luton’s impressive FA Cup run came to an end with a 3-0 defeat at home to Millwall. The nonleague side had stunned Norwich three weeks ago to reach this stage but found its Championship opponent one step too far at Kenilworth Road.

James Henry put the Lions in front after 12 minutes following a mistake by Janos Kovacs, with Rob Hulse adding another nine minutes before the interval from a tight angle. Dany N’Guessan then sealed the win with five minutes left to send Millwall through to the last eight.

A nonleague side has not made the FA Cup quarterfinals in 99 years.

Barnsley made it a hat trick of Championship teams in the quarterfinals with a 3-1 victory at League One’s MK Dons.

Chris Dagnall opened the scoring for the visitors after just three minutes before Marlon Harewood doubled the lead in the 20th minute.

MK Dons fought back in the second half with a goal from Dean Bowditch, but Dagnall’s second in stoppage time put the tie to bed. Alan Smith’s late dismissal rounded off a miserable afternoon for the home side.

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