When looking ahead to Sunday's meeting, Emery picked out the possible threats facing Villarreal, including that of Messi.
"Messi is going to have his connections on the pitch and his individual chances to score," Emery admitted.
"Whether that's with shots or his combinations with [Jordi] Alba, Sergi Roberto, [Antoine] Griezmann or just himself.
"He's a player who always causes problems and that's going to be the case for the whole 90 minutes.
"He's still a very tricky player [to face] - a player that we think has been and continues being the best in the world."