This study examines the taxonomy of pteropods and their divergence time using phylogenomics by incorporating 21 new species and new fossil evidence. In agreement with traditional taxonomy, we recovered the first molecular support for a division between sea butterflies (Thecosomata) and sea angels (Gymnosomata). Molecular dating demonstrated that these two lineages diverged in the early Cretaceous, and that all main pteropod clades, including shelled, partially-shelled and unshelled groups, diverged in the mid to late Cretaceous. This datasets includes the following files: 'pteropods_May18_s7.cali': fossil calibrations used for molecular dating 'Concat-Ptero200.phy.gz': reduced alignment with 200 marker genes showing highest support 'Concat-Ptero040317.phy.gz': main alignment of 2654 marker genes 'OMA-alis.tgz': individual alignments for each marker gene 'Ptero200_PBcatgtr.tgz': phylobayes run files on the reduced 200 genes dataset 'Ptero040317_examl.tgz': examl run files on the main 2654 markers alignment 'pteropods_May18_s7_cir_sb_bd.tgz'z: phylobayes molecular dating run with log-normal model 'pteropods_May18_s7_ugam_sb_bd.tgz': phylobayes molecular dating run with UGALM model