Ixobrychus cinnamomeus is a member of the large wading bird family, known as Ardeidae. In the present study, we determined the complete mitochondrial genome of I. cinnamomeus for use in future phylogenetic analysis. This circular mitochondrial genome is 17,180 bp in length and composed of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one putative control region. Three conserved domains and a minisatellite of 17 nucleotides with 22 tandem repeats were detected at the end of the control region. Phylogenetic relationships were reconstructed using the nucleotide and corresponding amino acid datasets of 12 concatenated protein-coding genes from the mitochondrial genome. Using maximum likelihood, maximum parsimony and Bayesian inference methods, the monophyly of Ciconiidae, Ardeidae and Threskiornithidae were confirmed; however, the monophyly of traditional Ciconiiformes and Pelecaniformes failed to be recovered. Although further studies are recommended to clarify relationships among and within the orders of Ciconiiformes, Pelecaniformes, Suliformes and Phaethontiformes, our results provide preliminary exploratory results that can be useful in the current understanding of avian phylogenetics.