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Finfish aquaculture supports epizootics due to high host density and the high biotic potential of these parasites. Reliable methods for parasite detection and identification are a necessary precursor to empirical assessment of strategies to mitigate the effects of these pathogens during aquaculture. We developed an integrative approach to detect and identify <jats:italic>Loma morhua<\/jats:italic> infecting Atlantic cod. We show that the spleen is more reliable than the commonly presumed gills as best organ for parasite detection in spite of substantial morphological plasticity in xenoma complexes. We developed <jats:styled-content style=\"fixed-case\">rDNA<\/jats:styled-content> primers with 100% sensitivity in detecting <jats:italic>L.\u00a0morhua<\/jats:italic> and with utility in distinguishing some congeneric <jats:italic>Loma<\/jats:italic> species. <jats:styled-content style=\"fixed-case\">ITS<\/jats:styled-content> sequencing is necessary to distinguish <jats:italic>L.\u00a0morhua<\/jats:italic> from other congeneric microsporidia due to intraspecific nucleotide variation. 64% of <jats:italic>L<\/jats:italic>.\u00a0<jats:italic>morhua <\/jats:italic><jats:styled-content style=\"fixed-case\">ITS<\/jats:styled-content> variants from Atlantic cod have a 9\u2010nucleotide motif that distinguishes it from <jats:italic>Loma<\/jats:italic> spp. infecting non\u2010<jats:italic>Gadus<\/jats:italic> hosts. The remaining 36% of <jats:styled-content style=\"fixed-case\">ITS<\/jats:styled-content> variants from Atlantic cod are distinguished from currently represented <jats:italic>Loma<\/jats:italic> spp., particularly those infecting <jats:italic>Gadus<\/jats:italic> hosts, based on a 14\u2010nucleotide motif. This research approach is amenable to developing templates in support of reliable detection and identification of other microsporidian parasites in fishes.<\/jats:p>","DOI":"10.1111\/jeu.12339","type":"journal-article","created":{"date-parts":[[2016,6,18]],"date-time":"2016-06-18T14:46:42Z","timestamp":1466261202000},"page":"67-77","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Integrative Approach for the Reliable Detection and Specific Identification of the Microsporidium <i>Loma morhua<\/i> in Atlantic Cod (<i>Gadus morhua<\/i>)"],"prefix":"10.1111","volume":"64","author":[{"given":"Aaron P.","family":"Frenette","sequence":"first","affiliation":[{"name":"Department of Biology University of New Brunswick Fredericton NB E3B 5A3 Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matth\u00edas","family":"Eydal","sequence":"additional","affiliation":[{"name":"Institute for Experimental Pathology at Keldur University of Iceland Keldnavegur 3 112 Reykjavik Iceland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haakon","family":"Hansen","sequence":"additional","affiliation":[{"name":"Norwegian Veterinary Institute Ullevalsveien 68, Pb 750 Sentrum N\u20100106 Oslo Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael D.B.","family":"Burt","sequence":"additional","affiliation":[{"name":"Department of Biology University of New Brunswick Fredericton NB E3B 5A3 Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael S.","family":"Duffy","sequence":"additional","affiliation":[{"name":"Department of Biology University of New Brunswick Fredericton NB E3B 5A3 Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2016,7,13]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/jfd.12372"},{"key":"e_1_2_6_3_1","first-page":"69","article-title":"Identification of gadoid species (Pisces, Gadidae) by PCR\u2010RFLP analysis","volume":"46","author":"Aranishi F.","year":"2005","journal-title":"J. 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