Non-metamorphic Palaeozoic sedimentary successions without major breaks exist in the Istanbul Zone of the Western Pontides (northern Turkey) and in the Taurides (southern Turkey). Based on different proxies, a Gondwanan affinity has been determined for the Taurides; however, the palaeogeographical position of the Istanbul Zone is still controversial. The aim of this paper is to discuss possible contributions of late Silurian and Devonian ostracods to the palaeogeographical assignment of the Western Pontides (Istanbul Zone). Furthermore, ostracods of the Taurides have also been evaluated in terms of the palaeogeographical setting of this terrane. Late Silurian ostracods of the Istanbul Zone (Western Pontides) show close similarities at the species level with the assemblage from the upper Silurian (Ludlow) rocks of Baltica. This Laurussian affinity indicates a palaeogeographical setting to the north of the Rheic Ocean for the Pontides during the late Silurian. The Devonian ostracod assemblages of both the Taurides and the Istanbul Zone have an affinity to both Laurussia and Gondwana. Therefore, a faunal link should exist during this long period between Laurussia and Gondwana. The faunal link between the two palaeocontinents can be explained on the one hand by a narrow ocean with shallow pathways. On the other hand, a wider ocean with long-shore currents, with broad and shallow shelf areas and/or islands functioning as stepping stones would also allow a faunal link for benthic ostracods.