Aspergillus niger is an important filamentous fungus used for the industrial production of citric acid. One of the most crucial factors that affect citric acid production is the amount of manganese present in the culture broth. Observations showed that the fungus develops a pellet-like morphology under manganese limitation conditions and that this limitation is decisive for high citric acid accumulation by A. niger. However, the exact mode of action of manganese in the cell is not clear. In this work, we show the impact of manganese ions on the citrate exporter encoding gene cexA and evaluate the citric acid production capability under wild-type and cexA overexpression conditions in the presence and absence of manganese.