Isolated islands and their often unique biota continue to play key roles for understanding the importance of drift, genetic variation, and adaptation in the process of population differentiation and speciation. One island system that has inspired and intrigued evolutionary biologists is the blue tit complex (Cyanistes spp.) in Europe and Africa, in particular the complex evolutionary history of the multiple genetically distinct taxa of the Canary Islands. Understanding Afrocanarian colonisation events is of particular importance because of recent unconventional suggestions that these island populations acted as source of the widespread population in mainland Africa. We investigated the relationship between mainland and island blue tits using a combination of Sanger sequencing at a population level (20 loci; 12,500 nucleotides) and next generation sequencing of single population representatives (>3,200,000 nucleotides), analysed in coalescence and phylogenetic frameworks. We found (i) that Afrocanarian blue tits are monophyletic and represent four major clades, (ii) that the blue tit complex has a continental origin, and that the Canary Islands were colonised three times, (iii) that all island populations have low genetic variation, indicating low long-term effective population sizes, and (iv) that populations on La Palma and in Libya represent relicts of an ancestral North African population. Further, demographic reconstructions revealed (v) that the Canary Islands, conforming to traditional views, hold sink populations, which have not served as source for back colonisation of the African mainland. Our study demonstrates the importance of complete taxon sampling and an extensive multi-marker study design to obtain robust phylogeographical inferences. This article is protected by copyright. All rights reserved.