We analyzed extra chromosomal genomes of avian blood protozoa, Leucocytozoon caulleryi. One of the genomes, the mitochondrial genome was completely sequenced resulting 5,959 bp in length. This genome contained the identical gene organization and contents to that of other avian blood protozoa previously analyzed: three functional genes for cytochrome c oxidase subunit I, III, and cytochrome b with following sets of discontinuous and scrambled 15 ribosomal subunit RNA genes. In addition, the mitochondrial genome was estimated to have the tandem repeated structure as well as previously found in avian Plasmodium species. Furthermore, we found partial gene sequences of apicoplast DNA, another extra chromosomal genome, from L. caulleryi. These sequences were estimated as partial caseinolytic protease C and elongation factor Tu A genes. This report is the first description of two extra chromosomal genomes of L. caulleryi.