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This book constitutes the proceedings of the 16th International Conference on Comparative Genomics, RECOMB-CG 2018, held in Magog-Orford, QC, Canada, in October 2018. The 18 full papers presented were carefully reviewed and selected from 29 submissions. The papers cover topics such as: genome rearrangements; genome sequencing; applied comparative genomics; reconciliation and coalescence; and phylogenetics.