And the Blackpool manager believes Paul Cook’s side are going to take some stopping in League Two.
It was the Tangerines who ran out 3-1 winners at Bloomfield Road last night as the Blues’ away struggles continued.
But Bowyer has no doubt about the quality of the side his players went up against.
And he is certain they will be in the shake-up come the end of the campaign.
Bowyer said: ‘In my opinion they are going to be very difficult to stop.
‘They were the best team we’ve played against this season.
‘So beating them should give us a boost and now the challenge is for us to not rest on our laurels.
‘Our players have to go out and reproduce that and more.
‘They will be there or thereabouts, 100 per cent.
‘They are an outstanding team and, given time, they will succeed.
‘Paul Cook has organised his team and got his recruitment right.
‘I think Portsmouth will become an example of what can happen given time.’
Bowyer reckons Pompey’s board deserve praise for sticking with Cook and giving him the chance to succeed – and feels they are an example to his club who have faced their own struggles in recent seasons.
Bowyer said: ‘I know Paul, but not as well as I know Leam (Richardson)and John Keeley obviously from Blackburn.
‘They are a big club, a fantastic club and they are an example to us in the sense we came down and are in this division for the first time in a long time.
‘We were in the Premier League not too long ago, the same as Portsmouth were. It takes time to rebuild and common sense has allowed Paul Cook to do that.
‘The recruitment they’ve brought in is fantastic and they are an unbelievable team.
‘Paul’s brilliant. I spent time in his company yesterday and I love his philosophy and the way they play.
‘It’s very hard work playing against him.
‘They are a terrific example to us, the best team we’ve played for sure.’
Bowyer is now looking for his side to take a leaf out of Pompey’s philosophy as they go to Crawley on Saturday.
He said: ‘I want us to be as dominant with the ball as Portsmouth are.
‘The table is looking a bit better now, but come back to me after 46 games.
‘We have to recover very quickly, debrief this game, put it to bed and prepare for Crawley.
‘We need to look at what we did well, where we need to improve, recover and then train on Friday before travelling on the beautiful M6 and M25 to Crawley!’