The Canary Islands were the first part of the Macaronesian archipelago to have been settled by humans. The various ways in which the indigenous inhabitants and later European colonisers interacted with the native and endemic flora is a central topic for archaeologists, geographers and ecologists. Floristic changes can be studied from phytoliths which are plant microfossils with a high potential for preservation in sediment deposits and they can help reconstruct past ways of life and vegetation changes through time. However, there is no comprehensive and systematic study and reference collection of phytoliths produced by the flora of the Canary Islands, so far. To make a start with a first phytolith reference collection of a selection of plants relevant for the study of past socio-ecological interactions there, we processed over a hundred modern plant specimens collected on the islands of Tenerife, Gran Canaria and La Palma to obtain the phytoliths from them, using the dry-ashing method. We then described the phytolith morphologies, and counted the numbers of morphotypes for each species. We have categorised taxa according to their phytolith concentration and production of morphotypes with diagnostic potential. Our results suggest that among the selected taxa, species within the Arecaceae, Boraginaceae, Cyperaceae, Poaceae and Urticaceae families are the main native producers of phytoliths in the archipelago. We also identified phytoliths with diagnostic potential in particular species within the Asteraceae, Brassicaceae, Cistaceae, Euphorbiaceae, Lamiaceae, Lauraceae, Ranunculaceae and Rubiaceae. We discuss how phytolith assemblages can be interpreted in archaeological sites and sediment records. Our growing reference collection is a significant step towards the application of phytolith analysis to disentangle the long-term climatic and human-driven transformation of this biodiversity hotspot, as well as the cultural use of plant resources.