Electric fishes are a diverse group of freshwater organisms with the ability to generate electric organ discharges (EODs) that are used for communication and electrolocation. Over 200 species have originated in South America, but of these, only a few have managed to colonize the Central American Isthmus. Here, we assembled two complete and one nearly complete mitochondrial genomes (mitogenomes) for three Central American Gymnotiformes: Sternopygus dariensis, Brachyhypopomus occidentalis and Apteronotus rostratus. We then explored the three species’ phylogenetic position in the context of South American electric fishes. Mitogenomes were organized in the standard fish mitogenome order, and presented sizes of 16,600, 16,540 and 15,940 base pairs (bp) (nearly complete) for S. dariensis, B. occidentalis and A. rostratus, respectively. We uncovered a novel 60 bp intergenic spacer (IGS) located between the COII and tRNALys genes, which appears to be unique to the Apteronotidae. Furthermore, phylogenetic relationships supported the traditional monophyly of Gymnotiformes, with the three species positioned within their respective family. In addition, the genus Apteronotus was placed as the basal taxon of the order. Finally, we found high sequence divergence (13.3%) between our B. occidentalis specimen and a sequence previously reported in GenBank, suggesting that the prior mitogenome of B. occidentalis represents a different South American species that was misidentified. Indeed, phylogenetic analyses using Cytochrome b gene across the genus placed the previously reported individual within B. bennetti. Our study provides novel mitogenome resources that will advance our understanding of the diversity and phylogenetic history of Neotropical fishes.