The most important Italian population of the Eurasian otter (Lutra lutra) occurs in the southern part of the peninsula with two isolated sub‐populations of about 250 adult individuals. The Eurasian otter is considered to be near threatened and it is a fully protected species. The aims of this study were to investigate for the first time the occurrence and characterize the parvoviruses included in the species Carnivore protoparvovirus 1 in seven carcasses of road‐killed Eurasian otters from the southern Italy. Carnivore protoparvovirus 1 are responsible for acute gastroenteritis and leukopenia in pets and free‐ranging carnivores. Initial screening of tissue samples by real‐time PCR revealed CPV/FPV DNA in tissue samples of five Eurasian otters; three of them, showed co‐infections by both CPV and FPV. Among the five positive Eurasian otters, we successfully obtained six DNA sequences from four individuals including two CPV‐2a, one CPV‐2b, one CPV‐2c, and two FPV sequences. Comparison of these sequences with 250 VP2 gene sequences deposited in the GenBank database, showed 10 nt differences resulting in two synonymous and eight non‐synonymous substitutions. On the basis of these results, two sequences here found were characterized as new CPV‐2a, one was characterized as new CPV‐2b variant, and one was characterized as FPV‐like mutant. The last two sequences belong to a FPV and CPV‐2c strain respectively. Carnivore protoparvovirus 1 is reported for the first time in the Eurasian otter showing high infection value in southern Italy. Occurrence of this infection should be studied further to understand its possible pathogenicity and virulence to the fragile and isolate Eurasian otter population which live in southern Italy.