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Atlantic sea scallop ( Placopecten magellanicus ) meats are normally firm and creamy white. However, scallops with small, darkened and stringy adductor muscle (gray meat) episodically occur along the Eastern Seaboard, most recently in the rotational management areas of Georges Bank after extended fishing closures. These gray meat scallops are associated with reduced harvestable biomass and mass mortality events. We tested age, nutritional stress and disease as causative agents for this condition. Adult scallops of different shell heights (SH) ranging from (90–145 mm) were collected from Georges Bank and analyzed for meat quality and the presence of pathogens using biochemical, histopathological and molecular methods. Gray meat occurrence was weakly correlated with shell height only explaining 8.49% of the variance in a generalized additive model (GAMS). Gray meat weights were lower than white meat (p < 0.001) and there was a dramatic reduction in protein content (p < 0.05) in gray meat scallops associated with extensive myodegeneration. Amino acid profiles confirmed the breakdown of muscle tissue with an increase in free hydroxyproline in gray meat scallops. Infection by an apicomplexan parasite was detected in the muscle tissue of all gray meat scallops tested. An intermediate pathology stage (brown meat) was also identified. As the parasitic infection increased, meat quality decreased. Numerous developmental stages of the parasite were present in various organs of the scallops. This apicomplexan has an identical SSU rDNA sequence to a novel parasite occurring in the Iceland scallop during a recent mass mortality event. The range of this parasite in Atlantic sea scallops and the effect of abiotic/biotic stressors on pathogenicity are currently unknown. Results from this study link an apicomplexan species, known to be highly pathogenic in scallops, to gray meat occurrence with a potentially high impact on the fishery. [ABSTRACT FROM AUTHOR]