Mosop, who won the Chicago race in October, has suffered an Achilles tendon injury that has ruled him out of the Games.
Double world champion Abel Kirui and Wilson Kipsang, who won the London Marathon in April, are the other members of the team.
"Emmanuel Mutai was among the six marathoners we named in the provisional team. We did not want to go outside that list, and we think Mutai is best placed for that assignment," Athletics Kenya secretary general, David Okeyo said.
"Mosop has had persistent Achilles tendon injury and we all thought it would heal. But he wrote a letter to us withdrawing from the team after it became apparent it would not heal in time for the Games."
Athletics Kenya will name the rest of the team for the London Olympics on June 23, except the women's 10,000 metres team which will be named at the east African nation's National Championships to be held later this week.