This dataset contains genotypic data for Ruditapes decussatus (European clam), including 13,438 SNPs genotyped across 213 individuals from seven geographically distinct populations with different levels of infection by Perkinsus olsenii. Genotyping was conducted using a high-throughput SNP array. Each individual is also associated with infection level data for Perkinsus olseni, a protozoan parasite of ecological and economic concern. The dataset enables analyses of population structure, local adaptation, and host-parasite interactions.