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We describe here the first fossil otoliths from the Middle Miocene (Badenian and Sarmatian) of Belgrade, Serbia. They were obtained from Lower Badenian outcrops at Slanci and from upper Badenian and Sarmatian sediments recovered from four shallow wells near the village of Barajevo. The otoliths from the Lower Badenian of Slanci represent fishes typical for an open marine environment, characterized primarily by the mesopelagic families Myctophidae and Bregmacerotidae, a faunal composition that is also well known from other time equivalent locations in the Central Paratethys. The upper Badenian and Sarmatian composition of the fish fauna, in contrast, is dominated by otoliths of the family Gobiidae, indicating a sharp environmental shift from open marine to shallow water, probably slightly brackish environments, which is also confirmed by the faunal composition of mollusks, foraminifera, and ostracods. Most of the gobiid genera identified in the samples from Barajevo represent small fishes of the so-called sand gobies with Ponto-Caspian affinities, such as Economidichthys, Knipowitschia , or Pomatoschistus , or are entirely endemic to the Ponto-Caspian Basin, such as Hyrcanogobius . Another group of endemic Ponto-Caspian gobies is the first fossil record interpreted to represent the genus Proterorhinus. These and other finds currently being investigated indicate that the origin of the extant, rich, endemic gobiid fauna of the Ponto-Caspian Basin dates back to a crucial time in the development of Paratethys during the Middle Miocene when it segregated from the Mediterranean with the onset of phases of low salinity in the basin. In addition, we briefly discuss the distribution of certain gobiid species during Late Badenian and Sarmatian as it begins to emerge. The following new taxa are described based on fossil otoliths: Hyrcanogobius hesperis n.sp. and Proterorhinus vasilievae n.sp.