Eastern lowland gorillas (Gorilla gorilla graueri) are the least studied of the three gorilla subspecies, particularly at the molecular level. We sequenced an internal region of the mitochondrial DNA cytochrome oxidase subunit II (COII) region and a hypervariable portion of the mitochondrial DNA control region (D-loop) from wild gorillas in both the montana and lowland habitats of KahuzI-Biega National Park, Democratic Republic of Congo. All individuals (n = 38) were identical at the COII region; this sequence indicates that diagnostic sites previously suggested for gorilla subspecies may be valid. Low variability was found within the D-loop region from a subset of the individuals (n = 15) sequenced for COII. Haplotype frequencies differed between the two habitats, suggesting a level of population subdivision that may have demographic consequences. These results also support the distinction of two distinct clades of gorillas comprised of western populations (G. g. gorilla) and eastern populations (G. g. grauerl and G. g. beringel). Future management of Kahuzi-Biega National Park should ensure that sufficient habitat remains to prevent further genetic isolation of gorillas in the montana section of the park.