The aim of the present investigation is a thorough inventory of the Harpacticoida (Copepoda) of the Portuguese islands Madeira and Porto Santo to provide a basis for comparisons of the harpacticoid faunas of successive elevations of the so called ‘Madeira Hot Spot Track’. Quantitative samples from 10 sampling locations at the coastlines of both islands were analysed (eight from Madeira and two from Porto Santo) and revealed a total of 27 families of Harpacticoida. Nine of the families were determined on species level comprising 43 species of which 31 were new to science. Comparisons of the family and species assemblages at the different Madeiran sampling locations indicate strong habitat heterogeneity as well as differences of the southern from all remaining locations. The sampling locations at the north and east coast are predominately characterized by interstitial taxa, those of the south coast by more robust burrowing or epibenthic taxa. Furthermore the two easternmost sampling locations of Madeira show clear similarity in terms of their harpacticoid assemblages with the sampling locations of Porto Santo. Eighty-eight per cent of the determined species of Porto Santo occur at the coast of Madeira as well (predominately at the easternmost sampling locations) indicating dispersal of Harpacticoida between both islands.