The circular mitochondrial genome of Naegleria gruberi is nearly 50 kbp in size.
Most genes are encoded on the same DNA strand and the standard genetic code is used.
In addition to this standard set, N. gruberi mtDNA contains numerous additional genes that are characteristic of plant and protist mitochondrial genomes, including genes encoding ribosomal proteins, additional subunits of the NADH dehydrogenase complex, and components of an ABC transporter. The order of ribosomal protein genes in N. gruberi mtDNA is reminiscent of the bacterial gene organization in the adjacent str , S10, spc and alpha operons.