He takes over the armband from Iniesta who left Barcelona to join Chinese club Vissel Kobe after a trophy-laden 22 years at the Nou Camp.
Sergio Busquets will be the vice-captain, with Gerard Pique and Sergi Roberto the third and fourth captains respectively.
Messi is Barcelona all-time goalscorer and he has won five Ballon d’Or with the Blaugrana.
Messi will be hopeful of lifting his first trophy as captain on Sunday as Ernesto Valverde’s side take on Sevilla in the Spanish Supercopa.
And with silverware having again evaded his grasp at international level during the World Cup, the five-time Ballon d’Or winner will be keen to be lifting more trophies over the next 12 months.
Barca lost just one match on their way to winning La Liga last term, and kick off the new season against Alaves on August 18.
The Catalan outfit also won the Copa del Rey last season, but Messi, in particular, was left disappointed as they crashed out of the Champions League at the quarter-final stage to Roma.
Valverde has moved to bolster his squad in a bid to secure more titles, with Malcom, Arthur, Clement Lenglet and Arturo Vidal all now forming part of the dressing room which Messi will be leading for the foreseeable future.