The Scotland international scored 28 goals in his debut season at Ewood Park and his exploits have alerted a number of Premier League sides.
Rhodes was an £8million signing from Huddersfield last year and Bowyer insists that the 23-year old is staying put.
"He's happy where he is," Bowyer told the Lancashire Telegraph.
"I spoke to him and I just wished him all the best as he went away for the international game before he comes back to us. Jordan is not for sale."
When asked if that was at any price, Bowyer said: "For me it is, certainly the conversation I had with the owners was that he was not for sale.
"You read about interest from Hull in the papers and you're always going to get speculation about your best players.
"Manchester United couldn't hang on to Cristiano Ronaldo, so every player has their price.
"There has been talk in the papers about Jordan and Martin Olsson as well, but these are some of our better players and we don't want to lose them."
Bowyer is also hoping to keep Ruben Rochina at Ewood Park, despite Real Zaragoza having the option of making the striker's loan spell permanent.
"I had a conversation with Ruben and I have outlined my plans to him," he said.
"We will have to see what happens now but I have told him that he is a player I think has a lot of ability. He has a fantastic left foot.
"Of course there are areas of his game he can still improve, but he is still a young lad."