There was an amateur team, called "Dzerzhinets", which played in the local competitions of the Odesa Oblast and Ukraine.

Professional football club was created in 1992 based on the amateur team – shortly after Soviet Union breakup in 1991.

[3] During the 2010–11 season Dniester started playing their home games in Odesa due to the unsafe state of their stadium (Viktor Dukov) in Ovidiopol.

[4] With the inability to secure finances to repair the stadium the club opted to move their head office to Odesa after the season.

[5][6] The club was relegated from Ukrainian First League after the 2012–13 season after losing a promotion/relegation playoff to Nyva Ternopil.