Many fans are glad to see the Spaniard go after a poor second half of the season.
The club announced the news in an official statement on their club website that Flores will leave the club after the game with Sunderland this weekend – with former Inter Milan boss Walter Mazzarri the favourite to take over.
Flores said regarding his decision to move on, as reported by the BBC:
"The club and me don't have the same point of view about the season.
"We don't have the necessary conditions to activate the clause to renew my contract so I will leave Watford as a consequence.
"I felt completely happy with this year and I have enjoyed this experience."
It is yet another managerial change for Watford, who have got through plenty of bosses in the Pozzo era.
Flores has delivered Premier League safety this season and took the club to an FA Cup semi-final so many fans are of the opinion that this is a big mistake from the board to not keep him on.
However, others are not too disappointed to see the back of Flores.
They have struggled for form since the turn of the year and Flores’ stubborn tactical play has not made him overly popular with sections of the club’s support. Many felt that keeping Flores would have been a precursor to a Premier League struggle last term.
It also seems that he and the board differed in opinion and that the relationship was now untenable.
Hopefully he will receive a warm goodbye on Sunday as Watford look toward the future.
Here is how fans reacted to the news on Twitter…
Thank you QSF! The memories for this season will never be forgotten #wfc— Jamie Donovan (@JamieD_96) May 13, 2016
To all of those at Vicarage Road, make sure we give QSF a send off, we are in the PL next year than an to him, let's not end it sourly #WFC— Watford FC I.M.O⚽️ (@IMOWatfordFC) May 13, 2016
#WatfordFC don't think it's a case of WFC not wanting QSF I think it's that QSF wanted to leave. Good luck to him & any departing player— iAmAHornet (@iAmAHornet) May 13, 2016
Pls just tell me this means the end for Jurado and Suarez #watfordfc— Gavin Smith (@wfcgls) May 13, 2016
QSF done a good job this season but the writing has been on the wall for a while now, sad to see him leaving all the same #WatfordFC— Scott Bradman (@SCB_14) May 13, 2016
Thanks for everything Quique! Some great memories this season #watfordfc— Rory M Tierney (@rorymtierney) May 13, 2016
Don't get me wrong, I'm gutted that it hasn't worked out with QSF because I love the bloke but it's the best thing for the club #watfordfc— Ben Fas (@bfas88) May 13, 2016