Hantaviruses are members of the family Hantaviridae and the order Bunyvirales, their genome consists of three single-stranded RNA segments categorized by size as small (S), medium (M), and large (L) segment. One of the members of this family is Orthohantavirus seewisense (SWSV) whose reservoir are shrews, and it has previously been detected in several European countries, including Slovenia and Hungary, countries neighboring Croatia. The tissues of nine shrews were used in this research. The presence of SWSV was confirmed in shrew tissue samples through the amplification of large (L) segment of the virus, and the first molecular characterization of SWSV in Croatia was performed. SWSV was confirmed in two out of nine shrew individuals, and the analyzed shrew species were reliably determined using mitochondrial markers. A sequence of the S segment and a partial sequence of the L segment were successfully obtained from the positive samples of the species Sorex araneus and Neomys anomalus. The confirmed presence of SWSV in Neomys anomalus in this research presents one of the rare findings of this virus in that shrew species. Moreover, phylogenetic analyses were performed by using Bayesian analysis and the Neighbor-joining method. The phylogenetic trees showed geographic-specific clustering of SWSV sequences. The SWSV sequences from Croatia were, as expected, grouped together with sequences from geographically close areas. The results of this research provide a basis for further investigations of this virus and its potential pathogenicity.