Anagenetic speciation is an important mode of evolution in oceanic islands, yet relatively understudied compared to adaptive radiation. In the Macaronesian region, three closely-related species of Artemisia (i.e., A. argentea, A. thuscula and A. gorgonum) are each endemic from a single archipelago (i.e., Madeira, Canary Islands and Cape Verde, respectively), representing a perfect opportunity to study three similar but independent anagenetic speciation processes. By analysing plastid and nuclear DNA sequences, as well as nuclear DNA amount data, generated from a comprehensive sampling in all the islands and archipelagos where these species are currently distributed, we intend to find common evolutionary patterns that help us explain the limited taxonomic diversification experienced by endemic Macaronesian Artemisia. Our time-calibrated phylogenetic reconstruction suggested that divergence among the three lineages occurred in a coincidental short period of time during the Pleistocene. Haplotype and genetic differentiation analyses showed similar diversity values among A. argentea, A. thuscula and A. gorgonum. Clear phylogeographic patterns – showing comparable genetic structuring among groups of islands – were also found within the three archipelagos. Even from the cytogenetic point of view, the three species presented similarly lower genome size values compared to the mainland closely-related species A. arborescens. We hypothesize that the limited speciation experienced by the endemic Artemisia in Madeira, Canary Islands and Cape Verde archipelagos could be related to their recent parallel evolutionary histories as independent lineages, combined with certain shared characteristics of seed dispersal, pollen transport and type of habitat.