"I don't want Kaepernick," Marshall said on ESPN's First Take. "I think he's good. My guy's Fitz. It's nothing against Kaepernick. ... I have my quarterback, so I'm good."
Kaepernick said earlier this week that he wants to leave the Bay Area and play for the Jets.
Marshall caught 109 passes for 1,502 yards and 14 touchdowns last season. Fitzpatrick, 33, completed 335-of-562 passes for 3,905 yards, 31 touchdowns and 15 interceptions for the 10-6 Jets.
Kaepernick, 28, completed 144-of-244 passes for 1,615 yards, six touchdowns and five interceptions in nine games this season.