Subgenus Lophuromys, L. aquilus species group (W. Verheyen et al., 2002). Described as a species, which was recognized in early checklists (G. M. Allen, 1939; Ellerman, 1940d), but subsequently included in L. flavopunctatus (Misonne, 1974; Musser and Carleton, 1993). Analyses of morphometric traits and mtDNA cytochrome b sequences by W. Verheyen et al. (2002) demonstrated the conspecificity of the synonyms with L. aquilus and definition of the species relative to others in the L. flavopunctatus complex of species. Geographic samples of L. aquilus form a monophyletic clade most closely related to a clade containing the Ethiopian L. brunneus and L. chrysopus, and Kenyan L. zena, both clusters considered to be members of the L. aquilus species group (W. Verheyen et al., 2002). Maddalena et al. (1989) reported chromosomal data for Burundi sample. Three-dimensional geometric morphometrics was used by Corti et al. (2000) to look at patterns of growth and cranial size and shape in L. aquilus (reported as flavopunctatus) compared with L. sikapusi and L. woosnami. Stanley et al. (2000) documented specimens from the Eastern Arc Mtns of Tanzania. Altitudinal distribution on Ugandan slopes of Ruwenzori Mtns reviewed by Kerbis Peterhans et al. (1998) in context of surveying small mammal distributions in those highlands (but samples from Ruwenzori Mtns are apparently a separate species in the L. aquilus group; W. Verheyen et al., 2002). Habitat and altitudinal distribution on Ugandan slopes of Mt Elgon recorded by Clausnitzer and Kityo (2001) and Clausnitzer et al. (2003; both as L. flavopunctatus).

The holotype of rubecula is from the Kenyan slopes of Mt Elgon. In the morphometric analysis by W. Verheyen et al. (2002), it clusters with holotypes of the Ethiopian L. chrysopus, and Cameroon L. dieterleni and L. eisentrauti, suggesting close affinity; however, the rest of their sample from Mt Elgon bunches with those identified as L. aquilus. Dieterlen and Gelmroth (1974) described L. cinereus from Marais Mukaba in Parc National du Kahuzi-Biega (Dem. Rep. Congo), which was recorded only from the type locality. It is morphologically closely similar to what they called L. flavopunctatus, and possibly only a gray morph of that species: "Es ist nicht auszuschließen, daß die vier als Lophuromys cinereus beschriebenen Stücke graue Farbmutanten von L. flavopunctatus sind" (Dieterlen, 1987:188). Identity of the holotype of cinereus with L. aquilus was confirmed by W. Verheyen et al. (2002).