This paper focuses mainly on the representatives of calcareous nannofossils and invertebrates from the Hrvaćani section of the Middle Miocene (Badenian) (Prnjavor Basin, southern margin of Pannonian Basin), and it defines the time of Badenian transgression in this area. Rich resources of fossil mollusk species, isolated parts of coral colonies, and other invertebrate remains were found in the investigated section. Moreover, turtle remains from marine sediments at the southern margin of Central Paratethys were recorded for the first time. Calcareous nannofossil biostratigraphy has established an NN5 Zone by the presence of Sphenolithus heteromorphus and the absence of Helicosphaera ampliaperta. The foraminifera associations from the analyzed sandstones belong to the Lower Badenian, namely the older zones of Ammonia viennensis and Elphidium crispum (the equivalent of Lagenidae Zone of Vienna Basin). The specimen of a turtle is currently attributed to order Testudines (suborder Pleurodira). From a stratigraphic and paleoecological point of view, all the fossil assemblages showed similar patterns for the subject of study, reflecting favorable conditions for developing a subtropical fauna in the open shallow marine environment. Consequently, by combining nannofossils, foraminifers, corals, malacological, and herpetological data, we can conclude that the early Middle Miocene (Badenian) in Hrvaćani (Bosnia) corresponds to the Lagenidae Zone (NN5 Zone) and was characterized by a relatively warm climate.