Orthohantaviruses are mainly carried and transmitted by wild rodents, although during the last decade, they have also been identified in multiple species of shrews and moles. Orthohantavirus, (Seewis virus, SWSV), first detected in Switzerland in a single (Eurasian common shrew) specimen, has been further described in several European countries, including Croatia's neighboring Slovenia and Hungary. Croatia is a well-known endemic region for several zoonotic agents including three different orthohantaviruses: (PUUV), (DOBV), and (TULV). In this study, nine shrews were tested and SWSV RNA was detected in liver, lung, and kidney belonging to two shrews (22.22%), one collected on Medvednica mountain in Zagreb County, and the other in the Stara Gradiška area in lowland Croatia. The phylogenetic analysis of the complete S segment's open reading frame (ORF) and partial L-segment revealed that the Croatian sequences, when compared to sequences from the adjacent geographic regions, form a specific genetic lineage. Two SWSV-positive shrew species- and (Mediterranean water shrew)-were identified using barcode-based sequence analysis. Therefore, the SWSV detection in throughout the course of this study is seen as a rare find in this shrew species. To our knowledge, this is the first molecular and phylogenetic analysis of SWSV in Croatia.