This dataset contains information on the infestation levels of Polydora sp. (Polychaeta, Spionidae) on Nodipecten subnodosus. In seven months between 2014 and 2015, 639 scallops were collected with snorkel and SCUBA diving in four natural banks (27°55´–27°35´N; 114°20’–113°50’W) from the Ojo de Liebre Lagoon, Baja California Sur, Mexican Pacific. The scallops were relaxed with a solution of magnesium sulphate and the blisters inside at each valve were counted and removed 2,170 invasive Polydora sp. worms, which also were fixed with formaldehyde 4% and preserved in ethanol 70%.