The 49ers ended the 2012 season with the NFL’s best backup quarterback.

Now, with super sub Alex Smith destined for Kansas City, they will enter free agency next month with one quarterback, Colin Kaepernick, who has thrown an NFL pass.

San Francisco’s backup quarterback, at the moment, is Scott Tolzien, who entered the league in 2011 as an undrafted free agent from Wisconsin. Tolzien, who has been active for two games in his two-season career, has the smarts and gym-rat mentality Jim Harbaugh covets in a quarterback, but lacks eye-popping physical skills.

The 49ers, of course, will provide competition for Tolzien, likely through both the draft and free agency.

The quarterback free-agent market is presently thin, with Miami’s Matt Moore and Carolina’s Derek Anderson among the names headlining the list. However, fallen-from-grace starters such as Arizona’s Kevin Kolb and Kansas City’s Matt Cassel could be cut in cost-slashing moves. Another possibility is Browns quarterback Josh Johnson, who was among the 49ers’ final roster cuts last summer and played for Harbaugh at the University of San Diego.

The trade of Smith to the Chiefs will free $8.5 million in salary-cap space.

“They’re going to have enough money to get a bridge guy in free agency, if they don’t feel comfortable with Tolzien,” ESPN analyst and former 49ers backup quarterback Trent Dilfer said. “Kevin Kolb, if he becomes available. Matt Cassel’s not a bad quarterback, especially in a backup role. There’s going to be market guys in free agency that are going to be really, really good fits. So they’re in a great position as far as backup quarterback, even though he’s not on the roster.”

With at least 15 draft picks, the 49ers also figure to identify a developmental quarterback in the draft. Dilfer, who is in the process of studying the quarterback class, agrees the draft lacks elite, ready-to-start talent. However, he believes it’s deep in intriguing prospects that need some grooming.