The FC Baia Zugdidi was founded in 2006. In 2009, FC Baia Zugdidi won promotion to the Umaglesi Liga.
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Below is a complete record of how many teams have played in each season throughout the league's history:
FC Baia Zugdidi took the place of the predecessor. Before the 2012–13 season the club changed its name from FC Baia Zugdidi to FC Zugdidi.
The climate in the town is subtropical humid, with an average temperature of +25 °C for the summer and -2 °C for the winter. It very often rains here – about 1500 mm of rainfall in a year.
In July 2006, FC Zugdidi and FC Mglebi Zugdidi merged. FC Mglebi Zugdidi played in Regionuli Liga. The club continued to perform in Pirveli League, but was called FC Mglebi Zugdidi. In the season 2006–07, won first place and returned to Umaglesi Liga. After the completion of the 2008–09 season came in seventh place, but for financial reasons has been resolved.
The women's team participated in the 2010–11 UEFA Women's Champions League qualifying round, where it lost all three matches.
FC Zugdidi is a Georgian football club based in Zugdidi.