African savannah elephants (Loxodonta africana) are an ecologically and economically important species in many African habitats. However, despite the importance of elephants, research on their parasites is limited, especially in wild populations. Currently, we lack genetic tools to identify elephant parasites. We present genetic markers from ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA) to identify five elephant-specific nematode parasites in the family Strongylidae: Murshidia linstowi, Murshidia longicaudata, Murshidia africana, Quilonia africana, and Khalilia sameera. We collected adult nematodes from feces deposited by wild elephants living in Amboseli National Park, Kenya. Using both morphologic and genetic techniques, we found that the internal transcribed spacer (ITS) region in rDNA provides a reliable marker to distinguish these species of strongyles. We found no evidence for cryptic genetic species within these morphologic species according to the cox-1 region of mtDNA. Levels of genetic diversity in strongyles from elephants were consistent with the genetic diversity seen within other strongyle species. We anticipate that these results will be a useful tool for identifying gastrointestinal nematode parasites in elephants.