Filamentous cyanobacteria have substantial niche overlap, and the causal mechanism behind their succession remains unclear. This has practical significance since several filamentous genera are the main producers of the musty odorant 2-methylisoborneol (MIB), which lead to odor problems in drinking water. This study investigates the relationships between two filamentous cyanobacteria, the MIB-producing genus Planktothrix and the non-MIB-producing genus Pseudanabaena, in a drinking water reservoir. We firstly identified their niche characteristics based on a monitoring dataset, combined this information with culture experiments and developed a niche-based model to clarify these processes. The results reveal that the optimal light requirements of Pseudanabaena (1.56 mol m$^{−2}$ d$^{−1}$) are lower than those of Planktothrix (3.67 mol m$^{−2}$ d$^{−1}$); their light niche differentiation led to a fundamental replacement of Planktothrix (2013) by Pseudanabaena (2015) along with MIB decreases in this reservoir during 2013 and 2015. This study suggests that light is a major driving force responsible for the succession between filamentous cyanobacteria, and that subtle niche differentiation may play an important role in shaping the filamentous cyanobacterial assemblages that drives the MIB odor problems in drinking water reservoirs.