There is a growing interest in the use of high-throughput genotyping methods for unraveling the genomic bases of animal resilience to environmental stress or infectious diseases, particularly in non-model species. The decrease in sequencing costs made these technologies within reach, leading to an increase in the number of genomes assembled at a chromosome level, making comparative analyses between species more accurate. Here, we sequenced the complete genomes of the hard clam, Mercenaria mercenaria, and its parasite QPX (Quahog Parasite Unknown) responsible of severe losses in Northeastern states of the USA. Short and long-read sequencing methods were combined with the new Hi-C technology, allowing us to achieve the complete chromosomes for each species. As a result, 19 chromosomes of M. mercenaria were assembled for a total genome length of 1.85Gb. Around 29,000 coding genes were predicted, with the help of additional RNAseq data (92% of the genes having an assigned functional annotation). The QPX genome is 42.3Mb in length assembled into 42 scaffolds with an N50 of 1.9Mb. These findings are in line with those obtained in other members of the Labyrinthulomycota family, which are known to have a large number of chromosomes. Having high-quality genomes for both the clam and its parasite opens the door for exciting research to unravel specific genomic features in each phylum, but also on the identification of pathways involved in the host-parasite interactions that take place during infection.