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Aim: Islands are often hotspots of endemism due to their isolation, making colonization a rare event and hence facilitating allopatric speciation. Dispersal usually occurs between nearby locations according to a stepping‐stone model. We aimed to reconstruct colonization and speciation processes in an endemic‐rich system of land‐based islands that does not seem to follow the obvious stepping‐stone model of dispersal. Location: Five land‐based habitat archipelagos of limestone outcrops in the floodplain of the Kinabatangan River in Sabah, Malaysian Borneo. Methods: We studied the phylogeography of three species complexes of endemic land snails, using multiple genetic markers. We calculated genetic distances between populations, applied beast2 to reconstruct phylogenies for each taxon and subsequently reconstructed ancestral ranges using 'BioGeoBEARS'. Results: We found spatial‐genetic structure among nearby locations to be highly pronounced for each taxon. Genetic correlation was present at small spatial scales only and disappeared at distances of 5 km and above. Most archipelagos have been colonized from within the region multiple times over the past three million years, in 78% of the cases as a result of long‐distance dispersal (LDD) or dispersal from non‐adjacent limestone outcrops. The flow of the main geographical feature within the region, the Kinabatangan River, did not play a role. Main conclusions: Phylogeographic structure in these Bornean land snails has only partly been determined by small‐scale dispersal, where it leads to isolation‐by‐distance, but mostly by LDD. Our results demonstrate that island endemic taxa only very locally follow a simple stepping‐stone model, whilst dispersal to non‐adjacent islands and especially LDD, is most important. This leads to the formation of highly localized, isolated "endemic populations" forming the onset of a complex radiation of endemic species. [ABSTRACT FROM AUTHOR]