With more than 33,000 sting cases and 47 deaths recorded between 2000 and 2016, Panama is the country with the highest incidence of envenomations by scorpions in Central America. Species in the genus Centruroides are responsible for most scorpion sting reports, however, identification at the species level is complicated because the genus has considerable intraspecific morphological variation. To date no molecular data have been reported from Panama that would help to estimate their genetic diversity and validate morphometricidentification methods. We provide here the first genetic diversity data of the two endemic species (C. granosus and C. panamensis) and other two species reported in Panama (C. bicolor and C. limbatus). A total of 41 specimens were sequenced for COI and 16S rDNA mitochondrial genes. The phylogenetic concatenated analysis separates the Panamanian samples into four well-supported clades represented by C. bicolor, C. granosus and (C. panamensis + C. limbatus). The two endemic species are not the closest relatives in the tree. Low diversity in combination with its very narrow distribution suggest that C. panamensis is susceptible to environmental degradation. A single specimen of Coiba island is intermediate in the tree structure between C. bicolor and C. panamensis and may represent an early stage of speciation. The haplotype network is also consistent with the phylogenetic trees.