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Coatis are traditionally divided into two genera (Nasua and Nasuella). Coatis from the lowlands of the Neotropics are larger (Nasua nasua in South America and Nasua narica in Central America) than those from the highlands in the Andean Cordilleras (Nasuella olivacea and maybe Nasuella meridensis). Some authors have claimed that Nasuella should be included in Nasua but strong data have not been provided to support this statement. We reported an extensive mitochondrial (mt) DNA analysis with 205 specimens with complete mitogenomes. Some N. olivacea were intermixed among haplogroups of N. nasua, some haplotypes of N. narica were intermediate between N. nasua and the most recent haplotypes of the Central American N. narica, and N. narica from southern Central America and northern Colombia were introgressed with mtDNA from N. olivacea. Furthermore, the spatial genetic structure of N. nasua, N. narica, and N. olivacea were practically identical. Additionally, we also show, for first the time, the karyotype of N. olivacea. The chromosome morphology of N. olivacea was un-differentiable from that of N. nasua. These data fail to support the independence of these two genera.