Rovers take on Millwall at Ewood Park this Saturday, but there are particular games from the four between the two sides during the last campaign that stand out for the manager.
"In the league at Ewood they won with two stunning strikes from what I can remember," said Bowyer.
"Then they came here in the replay of the FA Cup and knocked us out which was a bitter blow for the club because obviously there was a semi-final place at stake at Wembley.
"I know a lot of our lads were hurting, and are still hurting from that."
Bowyer wasn't in charge for the two cup games and the league meeting at Ewood, but took the reigns a month before an important league match at the Den three games from the end of the 2012/13 season.
"We then went down to Millwall and we had a fantastic performance and result there at the back end of the season which ultimately secured us the position in this league," recalls Bowyer.
"We knew it was our game in hand, we knew we had to win it and if we won it it would give us the a massive chance of staying in the division. That was our ultimate aim at the time.
"We went 1-0 down so to come back with the performance that we put out there in the second half was very good at a very tough place to go."
Tickets for this Saturday's match at Ewood Park against Millwall are currently on open sale with prices from £15 Adults, £10 Seniors and £5 Juniors.
Book online today at www.onerovers.co.uk
and collect your tickets from the Blackburn End collection point on the day of the game.