The paleontological collection of the Nature Research Centre in Vilnius (Lithuania) is among the oldest and most extensive in the country, both in terms of taxonomic diversity and specimen numbers. Throughout the 20th century, local geologists and paleontologists carried out extensive fieldwork, collecting material from within Lithuania as well as abroad. Thanks to their efforts, the Centre now houses a vast collection encompassing macro-, micro-, and nanofossils that represent a wide range of marine faunal groups. Although the exact number of specimens remains uncertain, archived catalogues suggest that the collection may include up to 200,000 fossils. Here, we present the most significant micropaleontological groups—gastropods, ostracods, foraminifera, acritarchs, acanthodians, and conodonts—illustrated with tables, figures, and supplementary files. Additionally, we provide an overview of the current status of these collections and discuss their future prospects in both scientific research and educational initiatives for schools and the wider public.