AlphaCoV and lineage C betaCoV, genetically similar to those identified in Spanish related bat species, have been detected in Italian Myotis blithii and Eptesicus serotinus, respectively, out of 75 anal swabs collected from Vespertilionidae between 2009 and 2012. Sequence analysis of the 816-bp obtained RdRp sequence fragment indicates a 96.9 % amino acid identity of the Italian lineage C betaCoV with the recent Middle East Respiratory Syndrome Coronavirus (MERS-CoV, Genbank accession number KF192507). This is the first documented occurrence of a lineage C betaCoV in the Italian bat population, notably in E. serotinus.