The Canary Islands are characterised by an outstanding level of biodiversity with a high number of endemic taxa. The Canarian avifauna is no exception and six extant avian species are recognised as endemic. However, we have a limited understanding of the genetic structure of these taxa, which makes it difficult to identify conservation priorities based on the existence of unique lineages. we analysed the diversification process and demography of the Canary Islands Chiffchaff Phylloscopus canariensis using two mitochondrial genes (cytochrome b and cytochrome oxidase subunit I). Although the species colonised the Canary Islands during the early Pleistocene, our results suggest a recent process of differentiation, which ran in parallel to the Last Glacial Maximum. Chiffchaffs from Gran Canaria emerge as a unique lineage since none of the haplotypes found on this island were recorded anywhere else in the archipelago. Our findings suggest a process of divergence according to the gradual colonisation and subsequent isolation of nearby islands. Demographic results show a stable trend of Chiffchaff populations until the colonisation of Gran Canaria (ca. 15,000 years ago), where the species significantly increased its effective population size. Nowadays, the effective population size of the Canary Islands Chiffchaff is stable, which highlights the ability of Chiffchaffs to adapt to local disturbances related to human activities. Overall, our results provide a scenario of incipient differentiation of the Canary Islands Chiffchaff and, importantly, underscore once more the role of Gran Canaria in driving speciation processes in this archipelago.—Illera, J.C., Ramírez, A., Rodríguez, L., Polypathellis, K. & Pérez-Tris, J. (2020). Maternal genetic structure reveals an incipient differentiation in the Canary Islands Chiffchaff Phylloscopus canariensis. Ardeola, 67: 401-414.