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Haptophyta encompasses more than 300 species of mostly marine pico‐ and nanoplanktonic flagellates. Our aims were to investigate the Oslofjorden haptophyte diversity and vertical distribution by metabarcoding, and to improve the approach to study haptophyte community composition, richness and proportional abundance by comparing two  rRNA  markers and scanning electron microscopy ( SEM ). Samples were collected in August 2013 at the Outer Oslofjorden, Norway. Total  RNA / cDNA  was amplified by haptophyte‐specific primers targeting the V4 region of the 18S, and the D1‐D2 region of the 28S  rRNA . Taxonomy was assigned using curated haptophyte reference databases and phylogenetic analyses. Both marker genes showed Chrysochromulinaceae and Prymnesiaceae to be the families with highest number of Operational Taxonomic Units ( OTU s), as well as proportional abundance. The 18S  rRNA  data set also contained  OTU s assigned to eight supported and defined clades consisting of environmental sequences only, possibly representing novel lineages from family to class. We also recorded new species for the area. Comparing coccolithophores by  SEM  with metabarcoding shows a good correspondence with the 18S  rRNA  gene proportional abundances. Our results contribute to link morphological and molecular data and 28S to 18S  rRNA  gene sequences of haptophytes without cultured representatives, and to improve metabarcoding methodology.

Haptophyte Diversity and Vertical Distribution Explored by 18S and 28S Ribosomal RNA Gene Metabarcoding and Scanning Electron Microscopy