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Sapajus flavius has been listed on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. The complete mitochondrial genome sequence of Sapajus flavius is presented here first, sequenced by next-generation sequencing (NGS). The Sapajus flavius mitogenome is 16,543 bp long, contains 13 protein-coding genes (PCGs), 2 rRNA genes (12S rRNA and 16S rRNA), 22 transfer RNA (tRNA) genes, and one control region (D-loop). The complete mitochondrial genome sequence provided here could help in the study of ecological and evolutionary research of Sapajus and conservation genetics of S .flavius ., Competing Interests: The authors report no conflicts of interest, and are alone responsible for the content and writing of the paper., (© 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)