Pteropods, holoplanktonic gastropods, play pivotal roles in marine ecosystems as integral components of food webs and carbon cycling. With global change threatening pelagic ecosystem equilibrium, conserving pteropod biodiversity is paramount. Here, we present the most extensive phylogenetic study of the order Pteropoda to date, utilizing a complete mitogenome phylogeny to support the suppression of Thecosomata, thus demonstrating the lack of relationship between Pseudothecosomata and Euthecosomata. Through multilocus Sanger-based taxon sampling with 411 specimens (92 newly sequenced), representing nearly 100 species (out of 163 valid) from various oceans, we elucidate robust support for higher taxonomic rankings. Despite strong support, relationships between the major groups Gymnosomata, Pseudothecosomata, and Euthecosomata remain contentious. Our study addresses unresolved taxonomic questions, identifying cryptic species complexes across vast biogeographic areas, and offering unprecedented insights into pteropod diversity. We shed light on several open questions in pteropod systematics, proposing the reclassification of L. antarctica stat. rest. and elucidating the position of Thliptodon, Heliconoididae, and Thieleidae. This systematic review enhances our understanding of pteropod diversity and underscores the urgency of conservation efforts in the face of changing oceanic conditions.
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