Collodaria are ubiquitous and abundant marine radiolarian (Rhizaria) protists (Biard et al. 2015). They occur as large colonies (a few millimeters up to 3 meters long) or as solitary specimens. Collodarians are known to play an important role in oceanic food webs both as active predators and as hosts of intracellular endosymbiotic microalgae primarily belonging to the dinoflagellate genus Brandtodinium. Despite their important ecological roles, very little is known about their diversity and evolution. Taxonomic delineation of collodarians is challenging and only a few species have been genetically characterized. Most Collodaria form colonies comprising tens to hundreds of individual radiolarian cells (i.e. central capsules) embedded in a gelatinous matrix. Each central capsule contains genomic DNA of the Collodaria host while the gelatinous matrix which also contains the DNA of prey and symbionts. Some species build a shell-like skeleton aroundtheir central capsule while others have siliceous spicules, similar to those in sponges, in the matrix, and some lack mineral structures altogether. Current taxonomic classification reveals several clades : Sphaerozoidae (skeleton-less but spicule-bearing), Collosphaeridae (mix of skeleton-bearing and skeleton-less taxa), Collophidiidae (skeleton-less). The family Thalassicollidae is composed exclusively of solitary species. This protocol describes a method for isolating central capsules containing oly the genomic DNA of the collodarian host by removing prey and symbionts through targeted dissolution of the gelatinous matrix and removal all material outside of host central capsules.