Plankton images collected by Imaging FlowCytobot from 2006 to 2013 at the Martha’s Vineyard Coastal Observatory (Massachusetts, USA) were used to identify and quantify the occurrence of the diatom Guinardia delicatula and of a parasite that seems specific to this host. We observed infection with morphological stages that appear similar to the parasite Cryothecomonas aestivalis. Our results show that events during which infection rates exceed 10% are recurrent on the New England Shelf and suggest that the parasites are an important source of host mortality. We document a significant negative relationship between bloom magnitude and parasite infection rate, supporting the hypothesis that the parasites play a major role in controlling blooms. While G. delicatula is observed during all seasons, the infecting stages of the parasite are abundant only when water temperature is above 4°C. The anomalously warm water and small G. delicatula bloom during the winter of 2012 provided evidence that parasites can be active through winter if temperatures remain relatively high. As climate change continues, winter periods of water below 4°C may shorten or disappear in this region, suggesting that parasite effects on species such as G. delicatula may increase, with immediate impacts on their population dynamics.