Dreissena rostriformis bugensis, an invasive dreissenid that has rapidly expanded in Lake Geneva since its first detection in 2015, filters large volumes of water and can therefore reshape phytoplankton communities. This study aim to examine how its filtration and ingestion depend on food concentration and food type, by using two contrasting phytoplankton species: the unicellular green alga Chlamydomonas reinhardtii, used as a reference food source, and the filamentous and potentially toxic cyanobacterium Planktothrix rubescens, which is a dominant species in the phytoplankton community of Lake Geneva. In a first experiment, mussels were exposed separately to each alga across a gradient of six chlorophyll-a concentrations (2–100 µg L⁻¹) to characterise their functional response. Clearance rates and Ingestion rates were higher for C. reinhardtii than for P. rubescens at equivalent carbon concentrations, and ingestion of C. reinhardtii followed a Type III (sigmoidal) functional response, whereas no classical model between the three functional response types adequately described the concentration independent ingestion of P. rubescens. In a second experiment, mussel where fed with mixtures of the two species at three ratios (25:75, 50:50, 75:25 P. rubescens:C. reinhardtii) across the same concentration gradient. Selective feeding on C. reinhardtii persisted when it represented at least half of the diet, but this preference weakened when P. rubescens dominated the mixture. This suggest either a dilution effect or an inhibitory effect of the cyanobacterium on the overall filtration. Together, these results indicate that quagga mussels discriminate against P. rubescens, suggesting that their ongoing invasion of Lake Geneva may reinforce the dominance of this cyanobacterium, with implications for phytoplankton community structure in a lake already affected by climate change and incomplete winter mixing.