The Naegleria genome sequence has indicated that the amoeboflagellate contains actin and microtubule cytoskeletons, mitotic and meiotic machinery, and several transcription factors.

[5][6] Naegleria's mitochondria resemble the evolutionary intermediate thought to have occurred within the ancestor of all eukaryotes, because of its presence of mitochondrial Fe-hydrogenase and complete aerobic respiration system.

[5] Naegleria amoeba undergo a closed mitosis, in which the nuclear envelope doesn't break down, but still proceeds through the typical stages.

[5] Observations suggest that Naegleria is primarily an asexual organism that reproduces by division of its amoebae to produce substantial clonal populations.

However, analysis of the genome strain NEG-M revealed that it is a composite of two distinct haplotypes having arisen from an interbreeding population.