Collembola were studied in a well-preserved riverine section of the Prut River in the Republic of Moldova. The study was focused on species diversity and habitat preferences of the particular species at two localities. Riparian habitats of the Prut River near Branişte included open river bank, forest belt and meadow, and the shore of Lake Costeşti-Stânca included meadow, pasture and shrub vegetation. In total 77 collembolan species were recorded, of which Neanura moldavica and Arrhopalites prutensis were endemic to Moldova. Comparative analyses showed a specific community composition at Branişte, with Anurida ellipsoides and Mesaphorura macrochaeta being abundant on the river bank and Hemisotoma thermophila in the meadow. In contrast, the forest plantation at the same locality was similar to the shrub-land in Costeşti, with the common species Mesaphorura critica, M. yosii, Deutonura albella and Isotomiella minor. Hygrophilous species preferred the habitats of the river section in Branişte, with quiet backwaters, to the artificial shoreline of the large lake. Species diversity was relatively high in the natural meadow and forest in Branişte and also in shrub-land on the lake shore. The present study documented relatively high collembolan species diversity at the shoreline and running water sections in the upper catchment area of the Prut River in Moldova that involve naturally valuable inundated habitats of Eastern Europe.