There was speculation the two series would intertwine but the 48-year-old director-producer has quashed rumours, reported Contactmusic.
"We are following 'Guardians' at Shepperton (with 'Avengers 2') but we won't be swapping cast members. Every movie is its own thing and has to be. Unless I take a lot of peyote and write a very different draft. and I'm not ruling that out," Whedon said.
It was previously thought the characters in 'Guardians of the Galaxy', slated to release next year, starring Chris Pratt, Zoe Saldana as a team of extra-terrestrial crime-fighters, would be integrated into 'The Avengers' sequel, which is due to release in 2015.
"All of our movies are connected. We're created in a way that is connected to the movies that came before us and we're even more connected to 'The Avengers 2', which comes after us. In that respect, what we hope is that these characters continue and at some point in time they will all meet up with different characters throughout the galaxy," Gunn said.
The cast of 'The Avengers 2' is yet to be finalised but Robert Downey Jr, Chris Hemsworth, Chris Evans and Mark Ruffalo are most likely to return for the superhero movie.