Chlamydomonas reinhardtii is a unicellular eukaryotic alga that has been studied as a model organism for decades. Despite an extensive history as a model system, phylogenetic and genetic characteristics of viruses infecting this alga have remained elusive. We analyzed high-throughput genome sequence data of C. reinhardtii field isolates, and in six we discovered sequences belonging to endogenous giant viruses that reach up to several 100 kb in length. In addition, we have also discovered the entire genome of a closely related giant virus that is endogenized within the genome of Chlamydomonas incerta, the closest sequenced relative of C. reinhardtii. Endogenous giant viruses add hundreds of new gene families to the host strains, highlighting their contribution to the pangenome dynamics and interstrain genomic variability of C. reinhardtii. Our findings suggest that the endogenization of giant viruses may have important implications for structuring the population dynamics and ecology of protists in the environment.