Cafeteria roenbergensis is a heterotrophic nanoflagellate that represents a geographically widespread and ubiquitous species of marine zooplankton. Its phylogenetic position and the paucity of genomic data among unicellular heterotrophic grazers make C. roenbergensis an interesting object for genomic studies. Moreover, C. roenbergensis is a known host of Cafeteria roenbergensis virus (CroV), a giant virus of the family Mimiviridae. Recently, we showed that mavirus, a virophage of the family Lavidaviridae and an obligate parasite of CroV, readily integrates into the nuclear genome of C. roenbergensis. Here, we sequenced the genomes of four different C. roenbergensis strains carrying several new endogenous mavirus-like elements. We show that endogenous elements are prevalent in marine bicosoecids and likely play an important ecological role in host defense against lytic giant viruses.