The complete mitochondrial genome of the Critically Endangered southern purple-spotted gudgeon, Mogurnda adspersa, was determined for the first time using 1/8 of a 454 pyrosequencing plate. The mitogenome was assembled using the bioinformatic software MIRA. The M. adspersa genome organization was very similar to most vertebrates, being 16,523 bp in length. It contained 13 protein-coding genes, 22 transfer RNA, 2 ribosomal RNA genes, and 1 non-coding control region. The current methodology was effective to assemble the whole mitogenome using 2008 mitochondrial reads representing 0.23% of total genomic reads produced and providing average mitogenome coverage of 17.4 reads per site. The whole mitogenome sequence provided here is deposited in NCBI with the accession number KJ130031 and may benefit systematics studies and conservation programs of M. adspersa.