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The data presented here comes from samples collected as part of two recent research projects (ISLANDBIODIV and MACDIV), which aimed to understand the drivers of community assembly in Macaronesian islands. We applied the sampling protocol COBRA (Conservation Oriented Biodiversity Rapid Assessment, Cardoso 2009) in ten 50 m x 50 m native forest plots in the Azorean Islands of Pico (6 plots) and Terceira (10 plots) to assess the diversity of spiders species. Through this publication we contribute to the knowledge of the arachnofauna of the Azores, and more specifically, to that of the islands of Pico and Terceira. This dataset presents data generated from spider samples collected in 16 forest plots on the Azorean islands of Pico and Terceira. Of the 40 species collected, 16 were introduced, 13 endemic, seven native (five of them Macaronesian endemics) and four undescribed species. Although most of the species had been previously recorded on both islands, two of the introduced species were recorded in Pico for the first time.