The coach is not worried for Spain, despite its thrashing at the hands of Brazil in the Confederations Cup, and says he is refreshed following his break from football
The four-time Ballon d'Or winner will play alongside the 21-year-old this season following the Blaugrana's 57 million euro 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 are unfounded.
"Will Messi and Neymar work together? The best player of all time alongside a brilliant footballer? I’m sure they’ll work together," he told the press.
He also stressed his belief that Spain will rise again following its 3-0 thrashing to the Selecao in the Confederations Cup final.
"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."
Meanwhile, he believes Barcelona will also continue to flourish.
"Barca won 100 points last season, which is a tremendous feat," the Spaniard said. "[Johan] Cruyff’s philosophy lives on and they still have marvellous players."
Guardiola's return has roused interest among those who wonder how will he fare away from his familiar Camp Nou setting and the 42-year-old trainer says he feels refreshed after his break.
"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 organization."
Guardiola's first competitive match in charge will be on July 27 in the DFB-Supercup against Borussia Dortmund.