The 50-year-old former Paraguay boss was confirmed as the new Barca boss on Tuesday, succeeding Tito Vilanova, who stepped down from the role after one season in charge as he continues his battle with cancer.
Both Martino and Messi are from the Rosario region of Argentina and the four-time Ballon d'Or winner has admitted he is looking forward to working alongside the man nicknamed 'Tata' at the Camp Nou.
"What a wonderful surprise it has been that Martino was chosen to coach the team," Messi wrote on the social network site 'WeChat'.
Martino led Messi's former club Newell's Old Boys to the Argentinian Clausura title last season and the semi-finals of the Copa Libertadores, but recently severed ties with the club.
Martino held a farewell press conference in Rosario on Tuesday night, in which he declared his belief that Messi and his father Jorge played a key role in Barcelona appointing him as Vilanova's successor.
He said: "I have no doubts that Messi spoke with the club directors. I'm sure that Jorge and Leo have had some weight in this decision."