Koscielny refused to join the Premier League club on their U.S. tour amid British media reports linking the 33-year-old French centre back with a move to Ligue 1 sides Girondins Bordeaux and Olympique Lyonnais.
Emery had labelled him an "important player" earlier this week but has now openly admitted Koscielny could leave.
However, the 23-year-old Holding could step up to be one of Emery's "five captains" -- all able to wear the armband when called upon, the manager said.
"I want one English player in these five captains," Emery told a media conference in Los Angeles ahead of the International Champions Cup match against Fiorentina on Saturday.
"An English player who grew up in our academy can understand the English spirit and Arsenal values. These are the qualities and more [we want].
"We are really happy with his [Holding's] progress. We need his performances as a centre back. [Before] he had his injury he was really playing with big performances."