Chytrids infect and kill various phytoplankton. Studies of chytrids infecting cyanobacteria and microalgae have focused only on a few host-parasite systems (hosts mainly Planktothrix and Asterionella ). Here we focus on a newly isolated and recently described chytrid that infects the nitrogen-fixing filamentous cyanobacterium Dolichospermum . This species specializes in infecting heterocyst cells only and may therefore affect the nitrogen fixation process. We performed infection experiments where Dolichospermum was exposed to the chytrid under nitrogen-limited and nitrogen-replete conditions and quantified the effects of infection on host nitrogen fixation and growth. Chytrid infection strongly decreased host growth under nitrogen-limited conditions, but not under nitrogen-rich. This was because the cyanobacterium could only obtain nitrogen from its partially infected heterocysts, which, despite the parasitism, retained some capacity for nitrogen fixation under nitrogen-limited conditions, but at a reduced level. Host filaments partially compensated for chytrid infection by increasing nitrogen fixation rates nearly 8-fold in the remaining heterocysts that survived infection. Nitrogen fixation rates were reduced by ⁓50% in infected Dolichospermum when normalized to biovolume, compared to uninfected controls. This reduction in the supply of nitrogen through nitrogen fixation and cyanobacterial development suggests that chytrid parasites may shape cyanobacterial bloom development and nitrogen fixation in nature.