The former Barcelona coach is confident the two players will click, and says he is not worried about the future of Spanish football after La Roja's Confederations Cup failure
The four-time Ballon d'Or winner will play alongside the 21-year-old this season following the Blaugrana's £48 million signing of the Brazilian from Santos earlier in the summer.
Guardiola, who left the Catalans at the end of the 2011-12 season but returned to the sidelines with Bayern Munich this June, thinks that some fans' fears that the duo will not gel will not be realised and stressed his belief that Spain will rise again following their 3-0 thrashing to the Selecao in the Confederations Cup final.
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"Will Messi and Neymar work together? The best player of all time alongside a brilliant footballer? I’m sure they’ll work together.
"Barca and Spain have got a lot of longevity. It’s not unusual that Spain lost [to Brazil], they had to at some point. Age will always catch up with you at some point but the national team have a bright future. Spanish football coaches work very well with the youngsters and with the talent there is out there, so I'm not worried."
Guardiola's return has roused interest among those who wonder how will he fare away from familiar Camp Nou settings and the 42-year-old trainer says he feels refreshed and is excited to be at the Allianz Arena.
"I was simply tired after four years of coaching Barcelona," he added. "I hadn’t rested, I needed a break. If I still needed a break, I would be very far away from the dugout.
When asked why he chose the Bundesliga to return to, he responded: "It was Bayern that chose me, and I loved their players and the German organisation."
Guardiola's first competitive match in charge will be on July 27 in the DFB-Supercup against Borussia Dortmund.