Florida Atlantic University's baseball program began in 1981 and has seen success, growth and change in its 41 seasons of competition.

The student-body decided "Owls" should be the athletic logo and in 2005, the baseball team lost its previous identity of "Blue Wave."

FAU continued to win its first five games of the season, including another major upset, this time on the road at another in-state super-power, defeating University of Miami Hurricanes, 11–10.

The Blue Wave finished the 1984 season with a record of 40–15, ranked 8th in the nation in the final NCAA Division II poll.

Since the hiring, FAU has won 61% of their games and transformed itself from a local power in South Florida to a national baseball program on the Division I level.

Cooney has led the charge for FAU baseball to enjoy such successes as, 67 athletes turning professional (with 4 reaching the majors).

[2] On March 15, 2006, against Columbia University, Cooney reached a personal milestone, coaching a team to his 800th career victory.

17 players from FAU baseball have won recognition as "All-American": Keith Foley (1983), Mike Ryan (1984), Scott Hay (1986), Jack Penrod (1988), Todd Moser (1999), Dan Jackson (1999), Dickie Hart (1999), Randy Beam (2003), Jeff Fiorentino (2004), Mickey Storey (2005), Robbie Widlansky (2007), Mike McKenna (2008), Andy Mee (2010), Hugh Adams (2013), Brendon Sanger (2015), Rickey Santiago (2015), C.J.

[4] 8 players from FAU baseball have won recognition as "Freshmen All-American": Kevin Connacher (1994), Rusty Brown (2001), Chris Pillsbury (2001), Jeff Fiorentino (2002), Derek Hutton (2002), Tim Mascia (2003), Mickey Storey (2005), Stephen Kerr (2014).