Iniesta had been at the club all of his 22-year career, breaking fully into the team in the 2004-05 season.
Sergio Busquets will now occupy the position as vice-captain while Gerard Pique and Sergi Roberto have joined the four-man leadership team, with the quartet all graduating from the club's academy.
The forward, Barca's all-time record goalscorer with 552 in all competitions, already wears the armband for the Argentina.
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Messi, who was named Barcelona's second captain in 2015, will now replace Barca's former icon, Andres Iniesta in the role. The Spaniard will break past half a thousand appearances for Barcelona if he remains fit and uninjured throughout their multiple campaigns this season.
Messi, who has been at Barcelona since the age of 13, is one of four players to be given new responsibilities by the Catalan club. Piqué returned from Manchester United in 2008 and has been at the club ever since.
The five-time Ballon d'Or victor will be aiming to lift his first trophy as captain on Sunday when Ernesto Valverde's side take on Sevilla in the Spanish Supercopa.