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Simple Summary: We tested the usefulness of new analytical tools such as fuzzy set theory to reveal the hidden internal complexity of the geographic distribution of species. Fuzzy set theory replaces the crisp notion of presence/absence of a species, typical of species distribution atlases, with the fuzzy notion of favorability for the species occurrence. Species distribution ranges are then revealed as more complex than recorded presences suggest, and metapopulation theory, which predicts fragmented favorable patches with connectivity among them, can be operationally analyzed. We identified the favorable patches for 222 butterfly species in the Iberian Peninsula using high values of favorability. We calculated the cost of reaching any part of the territory from a favorable patch using low values of favorability and distance and computed the inverse as connectivity. Some of the favorable territories can be vacant patches but also belong to the metapopulation structure, as they may be recolonized. This information is relevant for territory management and biodiversity conservation, serving to justify the protection of new areas or the modification of contours of reserves based on the role they play for the populations of interest. Metapopulation theory considers that the populations of many species are fragmented into patches connected by the migration of individuals through an interterritorial matrix. We applied fuzzy set theory and environmental favorability (F) functions to reveal the metapopulational structure of the 222 butterfly species in the Iberian Peninsula. We used the sets of contiguous grid cells with high favorability (F ≥ 0.8), to identify the favorable patches for each species. We superimposed the known occurrence data to reveal the occupied and empty favorable patches, as unoccupied patches are functional in a metapopulation dynamics analysis. We analyzed the connectivity between patches of each metapopulation by focusing on the territory of intermediate and low favorability for the species (F < 0.8). The friction that each cell opposes to the passage of individuals was computed as 1-F. We used the r.cost function of QGIS to calculate the cost of reaching each cell from a favorable patch. The inverse of the cost was computed as connectivity. Only 126 species can be considered to have a metapopulation structure. These metapopulation structures are part of the dark biodiversity of butterflies because their identification is not evident from the observation of the occurrence data but was revealed using favorability functions. [ABSTRACT FROM AUTHOR]