Kaepernick, Johnson Will Battle for Job as 49ers' Backup Quarterback

It's possible that Johnson might be better short-term fit, while Kaepernick continues to develop for future

There’s no question that Colin Kaepernick figures in the 49ers’ long-term plans.

After all, the quarterback from Nevada was taken with the fourth pick of the second round of the NFL Draft in 2011 and immediately hailed as the quarterback of the future.

At Nevada, the 6-foot-4, 230-pounder was an athletic playmaker who became the first NCAA player ever to throw for more than 10,000 yards and run for more than 4,000 while guiding Nevada’s Pistol offense. He has a strong arm, quick feet and was a winner in college.

After the Niners drafted Kaepernick, 49ers head coach Jim Harbaugh raved about him, saying, “I love the way he competes,” while praising his arm and athletic ability.

But with training camp now in session in Santa Clara, Kaepernick likely faces a battle to retain his backup position to starter Alex Smith on the depth charts.

While Kaepernick may be the long-term solution, will he be the team’s short-term solution?

In a test between Kaepernick, newcomer Josh Johnson and Scott Tolzien – the Niners’ No. 3 QB last season in his rookie year out of Wisconsin – will Kaepernick show the 49ers that he’s their best option in 2012 if Smith were to go down with an injury?

Johnson, who was coached by Harbaugh at the University of San Diego and signed a two-year deal with San Francisco this offseason, comes to the Niners after four seasons in Tampa Bay, where he was the Bucs’ fifth-round pick in 2008. Over that time, Johnson has played 26 games (with five starts) completing 96 of 177 passes for 1,042 yards and five TDs, while also rushing 37 times for 237 yards. Like Kaepernick, he’s a good scrambler and runner and has good size (6-foot-3, 205 pounds).

It’s possible that Johnson’s experience might make him better suited for relief duty in 2012 while the Niners continue to give Kaepernick a chance to grow in his second season without throwing him into the fire. A recent story in the San Francisco Chronicle by Eric Branch noted, too, that Kaepernick struggled with his accuracy in minicamp.

Kaepernick, of course, wants to play and has been working this offseason to refine his mechanics. He’s been doing extra throwing even beyond the organized team workouts, with teammates at a park near the team’s practice facility.

“I just want to keep working on my feet, getting my feet (together) quicker, getting through reads quicker,” Kaepernick told reporters Tuesday. “Just taking pressure off the offensive line and getting the ball out of my hands.”

Kaepernick and Johnson have become friends, but Kaepernick knows it will be a competition with him to win that No. 2 job.

“Josh is a great guy,” Kaepernick said. “I’m good friends with him. But at the same time we know it’s a competition when we step on the field.”

Last season, though Kaepernick was given plenty of opportunities to play in the preseason, he played in just three regular-season games, throwing only five passes and completing three for 35 yards.

So, as far as knowing how far he’s progressed to play in game situations, it’s impossible to tell.

When Johnson was asked recently about the quarterback depth chart, he said he’s not thinking about battling Kaepernick and Tolzien.

“My mindset is to be in control of the offense and run the show,” he told Cam Inman of the Bay Area News Group. “When you’re under center it’s your offense. There’s only one quarterback out there at a time.”

The man on the bubble in the three-way competition could be Tolzien, who was picked up just before the start of last season after he was released by the Chargers, who had signed him as a free agent.

Tolzien didn’t see any regular-season action in 2011, although he had some good moments in the exhibition season, including a game against the 49ers when he completed 16 of 23 throws for 226 yards and a touchdown.

If Smith is healthy and Kapernick and Johnson are on the roster, will the 49ers keep Tolzien and carry four quarterbacks on the roster?

It should make for an interesting battle, to see how the three QBs fare in training camp and exhibition games.

“I don’t want to speak for all four of us, but I’m pretty sure that we’d all say the same thing,” Tolzien told Alex Espinoza of 49ers.com this week. “Individually, we’re all working to be the starter, because you’d be cheating yourself if you weren’t.”

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