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Abstract Members of the order Isochrysidales are unique among haptophyte lineages in being the exclusive producers of alkenones, long‐chain ketones that are commonly used for paleotemperature reconstructions. Alkenone‐producing haptophytes are divided into three major groups based largely on molecular ecological data: Group I is found in freshwater lakes, GroupIIcommonly occurs in brackish and coastal marine environments, and GroupIIIconsists of open ocean species. Each group has distinct alkenone distributions; however, only GroupsIIandIIIIsochrysidales currently have cultured representatives. The uncultured Group I Isochrysidales are distinguished geochemically by the presence of tri‐unsaturated alkenone isomers (C_37:3bMe, C_38:3bEt, C_38:3bMe, C_39:3bEt) present in water column and sediment samples, yet their genetic diversity, morphology, and environmental controls are largely unknown. Using small‐subunit (SSU) ribosomalRNA(rRNA) marker gene amplicon high‐throughput sequencing of environmental water column and sediment samples, we show that Group I is monophyletic with high phylogenetic diversity and contains a well‐supported clade separating the previously described “EV” clade from the “Greenland” clade. We infer the first partial large‐subunit (LSU)rRNAgene Group I sequence phylogeny, which uncovered additional well‐supported clades embedded within Group I. Relative to GroupII, Group I revealed higher levels of genetic diversity despite conservation of alkenone signatures and a closer evolutionary relationship with GroupIII. In Group I, the presence of the tri‐unsaturated alkenone isomers appears to be conserved, which is not the case for GroupII. This suggests differing environmental influences on Group I andIIand perhaps uncovers evolutionary constraints on alkenone biosynthesis.