Protists have representatives in all but one of the kingdoms in the tree of life and are highly important in the oceans, where they generate most of the carbon-flow in the first trophic levels. Parasitic lineages work as controlling factors in these ecosystems and cause varying effects in their hosts. The mesomycetozoans, X-cell, apicomplexans and microsporidia are such groups, all known members being parasites of a wide range of hosts. While for all mentioned groups at least some species are well described, the X-cell parasites are still mysterious. X-cell infects several groups of fish, although fish with a benthic ecology seem to be targeted more. The mechanism of transmission is nevertheless, still unknown as well as any other part of their life cycle. In order to investigate protists in the intestinal content of Gadus morhua, DNA was extracted, amplified and subsequently sequenced on Illumina MiSeq. To relate diversity to ecological factors, metadata was collected at sampling locations. Special focus was given to the protist groups Mesomycetozoa and X-cell. The intention of this study was to shed light on the diversity of protist parasites in the intestines of cod, and discuss potential transmission pathways of these parasites. A high diversity of protists was discovered in the intestines with representatives from most of the major kingdoms. 11 % of the Operational Taxonomic Units (OTUs) collected were from obligate parasite species. One of these was X-cell and taxonomy placement as well as phylogenetic analysis confirmed it as the Gadus morhua-infecting genotype. Three OTUs belonging to the Mesomycetozoa were also detected. Neither of the assigned species have been described as parasites of fish, but sequence variation in two of the OTUs indicate that they represent species not present in nucleotide reference databases. A large diversity of Apicomplexa as well as Microsporidia was also seen, constituting large parts of the dataset. This is the first time X-cell has been detected in intestinal content of fish, and its presence in the intestine could indicate that this is part of a transmission or infection pathway of X-cell. The small number of mesomycetozoans, and the genera found were surprising. Nevertheless, they could represent unknown parasites of fish. The large number of apicomplexans and microsporidians seen indicate they are significant parasites of cod in the Oslofjord.