Bayern won last seasonâ€™s European, German league title and German Cup (DFB-Pokal) treble under Jupp Heynckes but Mourinho is of the belief that Guardiola has taken them to an even higher level this term.
"I think Bayern are getting better and better," the Portuguese told Yahoo.
"I think this new Bayern started with Louis van Gaal.
"He started cleaning the team of all the players and starting with Thomas Muller, Bastian Schweinsteiger, Holger Badstuber and Toni Kroos, he was starting with these people and took the team to the Champions League final in 2010.
"After that came Jupp Heynckes, who did unbelievable work, and the team kept becoming better and better and they won the Champions League, and now Guardiola also is a fantastic coach and I think [they are] naturally improving.
"Over the last few years as a club they are doing very well."
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