A scalar magnetic anomaly map of the regions offshore the Canary Archipelago is presented here. This map is based on measurements taken inside the Exclusive Economic Zone Project framework. This paper contains a description of the data set, whose accuracy and internal consistency are analysed. The magnetic anomalies are described and the main structural trends are highlighted. This analysis has served to detect two possible fractures with a NW—SE component: one separates Fuerteventura from Gran Canaria Island, and the other apparently runs through Fuerteventura. The latter finding agrees with a 1.7 km depth offset, between its northern and southern halves, detected by the algorithm based on the Euler Deconvolution. A similar approach has been performed, estimating the depth to the top of the most significant anomalies. This result shows that the most noteworthy magnetic anomaly source of the archipelago, which lies between Tenerife and Gran Canaria Island, seems to be located at an average depth of 4 km below sealevel. A spectral analysis was performed to estimate the depth extent of the deepest anomalies. It argues the presence of sub-crustal magnetic sources (underplating) in the archipelago. A standard Euler Deconvolution analysis was executed to analyse the spatial distribution of these mantle-like sources. Our results seem to support the existence of magmatic underplating under Gran Canaria, Tenerife, and Fuerteventura, and suggest this possibility for La Palma.