We present the first record of the ant Pheidole megatron Fischer and Fisher, 2013 in Rwanda, a species thought to be endemic to the Malagasy region. Specimens were collected in July 2019, in one of the houses located at Kivumu, in the center of Rwanda. They were first morphologically identified as Pheidole megatron using a recent identification key. Molecular identification through mitochondrial cytochrome oxidase I (COI) confirmed the morphological identification. The Rwanda sample clustered with samples from the Comoros, and it belongs to the group megacephala. Future studies may focus on the biology and ecology of this ant species in Africa. Moreover, we suggest the screening of other African populations of Pheidole megacephala using finer genetic markers with higher mutation rates to clarify the identification and spread of the species.