Pochettino started the campaign by picking Kyle Walker and Danny Rose at right-back and left-back respectively, but the pair have now been challenged by Ben Davies and Kieran Trippier.
Davies and Trippier have been in fine form of late and Merson now feels that Pochettino does not know his strongest starting line-up.
“It’s not just that, it’s the way that they play,” Merson said. “They’re ask to go there and back for 90 minutes.
“The longer the season has gone on, they’ve had massive affects on the game, these full-backs.
“I don’t think he knows who are the best two, though. I honestly don’t think he knows.”
Pochettino’s rotation policy has paid dividends in recent weeks, as Spurs’ full-backs have all been integral.
Whoever plays on the left and right hand sides of defence are required to provide Tottenham with width, and their energy has been crucial.
Both Rose and Trippier have scored important goals for Spurs of late, to ensure that the North London side remain in title contention.
At the moment Tottenham are five points behind Leicester City, but their position in the top four looks very commanding.
Spurs’ next fixture comes on Thursday evening against Borussia Dortmund in the Europa League.