We sequenced the complete mitochondrial genomes of three pairs of congeneric peripheral fishes distributed on either side of the Isthmus of Panama in order to test their status as geminate species pairs. Our phylogenetic analysis did not support a sister relationship between Gobiomorus dormitor and G. maculatus and therefore they cannot be considered geminates. The average genetic distance of protein-coding genes between Sicydium altum and S. salvini was more than two times larger than between Atlantic and Pacific Awaous banana, suggesting different timings for their divergence across the Isthmus of Panama.