Anomaluroidea, commonly known as the “scaly-tailed squirrels,” are an emblematic group of tropical African mammals that includes gliding forms. The family Anomaluridae was until recently represented by three genera: the flying scaly-tailed squirrels (Anomalurus), the flying mouse (Idiurus) and the flightless scaly-tailed squirrels (Zenkerella). Idiurus and Zenkerella have long been grouped into the Zenkerellinae subfamily, and Zenkerella was interpreted as a rare case of evolutionary reversal to non-gliding lifestyle. Recent studies have demonstrated that Zenkerella is sister to all other modern anomalurids, and represents in fact the monogeneric family Zenkerellidae. The Anomalurus genus was split into Anomalurus and Anomalurops, but no study has ever considered all Anomalurus species together in a phylogeny to test the status of Anomalurops. Here, we used mitogenomic next-generation sequencing to infer the phylogenetic relationships among all extant anomalurids and to estimate their divergence ages. We found that the arboreal Zenkerella is the sister group of all extant gliding anomalurids (Idiurus and Anomalurus). We confirmed that Anomaluroidea only evolved the gliding adaptation once. A comparison based on morphological traits indicates that Zenkerella harbours several unique morphological features. We propose new morphological characters for the novel classification of modern Anomaluroidea, which includes the families Zenkerellidae and Anomaluridae. Using different calibration schemes, we demonstrated that classical dating methods relying only on mitogenomes provide rather young Miocene estimates between Zenkerellidae and the Anomaluridae. The use of published nuclear genes, internal calibrations and tip dating converged towards an Eocene split between gliding and non-gliding scaly-tailed squirrels, which is in agreement with the African fossil record. Finally, we provide the first exhaustive species-level molecular phylogenetic inference for the genus Anomalurus. We found that Anomalurus beecrofti is the sister group of all other species of Anomalurus and branched off during the Miocene.