Small-ruminant lentivirus (SRLV) infections are widespread in Poland, and circulation of subtypes A1, A12, A13, A16, A17, B1 and B2 has been documented. The aim of this study was to characterize the SRLV strains circulating in sheep and goats in mixed flocks in the Malopolska region, where the highest seroprevalence has been detected. Phylogenetic analysis revealed that most of the isolates from sheep belonged to subtype A13, suggesting that this subtype may be predominant in the Malopolska region. Furthermore, the existence of a new subtype, tentatively designated as A18, was described for the first time. This work extends the current knowledge on the distribution of SRLV subtypes in sheep and goats in Poland and provides further information on the genetic diversity of SRLV. The new data are important for both epidemiological studies and eradication programs and provide insight into the evolution of SRLV.