Even for well-established insect model systems, such as the yellow dung fly Scathophaga stercoraria (Linnaeus) (Diptera: Scathophagidae), there may be hidden systematic ambiguities that require clarification. Dung flies from the Afrotropical Region have been considered (i) as con-specific and not different from all the other Holarctic Scathophaga stercoraria; (ii) as a local and peculiar African subspecies of S. stercoraria (Scathophaga stercoraria soror Wiedemann), or (iii) as a separate valid species (Scathophaga soror Wiedemann). Our study represents an attempt, based on mitochondrial (COI, 12S, and 16S), nuclear (ITS2) as well as microsatellite markers, to clarify this problem. Results strongly suggest that S. soror is a separate taxon from S. stercoraria. Due to the importance of S. stercoraria as a model system for studies in ecology, behaviour and evolution, the systematic position of S. soror (relative to S. stercoraria) is not solely of interest for systematists, but for evolutionary ecologists as well.