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Aim We test three alternative hypotheses for the disjunct Mediterranean-southern African distribution of endophagous weevils within the genera Rhinusa and Gymnetron (Coleoptera: Curculionidae): (1) a Palaearctic origin with dispersal to southern Africa; (2) a southern African origin with dispersal to the Palaearctic; and (3) a widespread ancestral distribution fragmented by vicariance. Divergence times are estimated to provide an approximate temporal framework for the evolution of the group and to evaluate potential palaeogeographical scenarios. Location Southern Africa, the Mediterranean region, the Palaearctic and eastern Africa. Methods Freshly collected and dry, pinned samples of weevils were used as a source of DNA. Prior genetic information was used to identify short phylogenetically informative amplicons within the 16S ribosomal RNA gene (16S). Phylogenetic reconstructions using Bayesian and maximum likelihood analyses of mitochondrial and nuclear DNA sequence data and molecular dating techniques were used to infer the biogeographical history of Rhinusa and Gymnetron species. A statistical approach to dispersal-vicariance analysis (s-diva) was used to further assess biogeographical hypotheses. Results Successful polymerase chain reaction amplification of targeted short 16S DNA sequences (150bp) from dry, pinned specimens provided for increased species sampling of Rhinusa and Gymnetron by 230%, greatly expanding species representation from southern Africa. Phylogenetic reconstructions and s-diva analyses support a southern African origin for Rhinusa and Gymnetron species. Divergence time estimates suggest southern African and Palaearctic lineages diverged c.11.6-7.4Ma. Main conclusions Rhinusa and Gymnetron represent a complex of lineages with a shared evolutionary history of range expansions from southern Africa into the Palaearctic. Our results support a late Miocene vicariance scenario, most likely as a result of repeated desertification. The use of prior genetic information to identify short phylogenetically informative amplicons offers a useful approach for molecular phylogenetic analyses incorporating archival material.