Neobatrachia is a phylogenetically-nested anuran group and contains approximately 85% of amphibian species. It is difficult to analyze the neobatrachian mitochondrial (mt) genome due to accelerated nucleotide substitution rates and occasional gene rearrangements. To overcome these problems, we designed 15 PCR primers. These primers, together with two primers from a previous study, could amplify almost the entire mt genome in all neobatrachians tested (seven species from seven different families) without optimizing PCR conditions. Among the tested taxa, Trichobatrachus robustus (Arthroleptidae) and Hyperolius viridiflavus (Hyperoliidae) showed unique amplification patterns, suggesting occurrences of gene duplication and/or rearrangements in these mt genomes.