Changes in size and shape in the skull of five species of the African rodent genusArvicanthiswere studied using Geometric Morphometrics, in an attempt to evaluate their systematics and taxonomy which is still confused. Four species endemic to the Horn of Africa (Aabyssinicus, A. dembeensis, A. blickiandA. somalicus)and a population of the’A. niloticus’complex from West Africa (Benin) were investigated. These species are widespread with ranges at very different altitudes, from arid grasslands up to the alpine moorlands at 4300 m a.s.l., and represent one of the major pests in croplands. Size and shape differences between species were compared with phylogeny (deduced from karyotype rearrangements), time of divergence (allozymes) and altitude. Morphometric divergence does not reflect any cladogenetic sequence and neither any association with altitude, but rather adaptive patterns that are unique to each species.