Quaternized polymers as polymer electrolytes enable the operation of alternative fuel cells under high pH conditions or anhydrous conditions to overcome the challenges of the proton exchange membrane fuel cells. Ionomer hydrophobicity derived from high fluorine contents is considered to be beneficial to electrode performance, but due to the synthetic difficulties, not many fluorinated quaternized ionomers have been reported with their influence on electrode behavior in these emerging fuel cells. In this presentation, we report a series of quaternized poly(fluorene)s with different levels of fluorine contents to study the impact of hydrophobicity to fuel cell performance and durability in different fuel cell operating conditions. The study of the fluorinated poly(fluorene) ionomers elucidates the precise control of electrode hydrophobicity for highly efficient and cost-effective fuel cell systems.