AbstractAscidians, or sea squirts, are sac‐like sessile tunicates commonly found in modern seas. Although the oldest ascidians, or at least ascidian‐like tunicates, are mid‐Cambrian in age, the quality of the ascidian fossil record is extraordinarily poor. It mostly consists of isolated finds or low‐diversity assemblages, often represented by mineral spicules. Our study reports the world's most diverse assemblage of ascidian spicules, originating from the Middle Miocene Bogutovo Selo near Ugljevik, Bosnia and Herzegovina. This material includes 31 spicule types, with four assignable to species (Lissoclinum cf. perforatum, Polysyncraton cf. bilobatum, Didemnum cf. vexillum and D. cf. leopardi) and 10 to genera, all belonging to aplousobranchiate ascidians. Comparing our findings with those of two other studies that use modern biological nomenclature, our assemblage shows a closer resemblance to the distant Eocene Australian assemblage than to the Miocene ascidians from Eastern Paratethys. This suggests the persistence of a once‐homogeneous and widely distributed Eocene fauna into the Miocene, while the Eastern Paratethyan basin developed an endemic fauna after the isolation of Eastern Paratethys from the open sea. Some taxa of our assemblage currently inhabit the Mediterranean Sea. The discovery of one species in distant South African waters suggests that tectonic and environmental changes during the Late Miocene, including the closure of the Gibraltar Strait and prior disconnection from the Indian Ocean, may have limited its survival to remote refugia. The study underscores the importance of including spicules in reconstructing ascidian faunas in the geological past, an area that has been surprisingly understudied.