| Summary: | Eastern oyster (<i>Crassostrea virginica</i>) aquaculture is increasingly playing a significant role in the state of Maine’s (USA) coastal economy. Here, we conducted a qPCR-based survey for <i>Haplosporidium nelsoni</i>, <i>Perkinsus marinus</i>, and <i>Perkinsus chesapeaki</i> in <i>C. virginica</i> (n = 1440) from six Maine sites during the summer–fall of 2016 and 2017. In the absence of reported die-offs, our results indicated the continued presence of the three protozoan parasites in the six sites. The highest <i>H. nelsoni</i> qPCR-prevalence corresponded to Jack’s Point and Prentiss Island (<inline-formula> <math display="inline"> <semantics> <mrow> <mover accent="true"> <mi>x</mi> <mo>¯</mo> </mover> <mo>=</mo> </mrow> </semantics> </math> </inline-formula> 40 and 48% respectively), both located in the Damariscotta River Estuary. Jack’s Point, Prentiss Island, New Meadows River, and Weskeag River recorded the highest qPCR-prevalence for <i>P. marinus</i> (32–39%). While the <i>P. marinus</i> qPCR-prevalence differed slightly for the years 2016 and 2017, <i>P. chesapeaki</i> qPCR-prevalence in 2016 was markedly lower than 2017 (<20% at all sites versus >60% at all sites for each of the years, respectively). Mean qPCR-prevalence values for <i>P. chesapeaki</i> over the two-year study were ≥40% for samples from Jack’s Point (49%), Prentiss Island (44%), and New Meadows River (40%). This study highlights that large and sustained surveys for parasitic diseases are fundamental for decision making toward the management of the shellfish aquaculture industry, especially for having a baseline in the case that die-offs occur.
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