Using molecular techniques, we documented the presence of Nosema ceranae in honeybees (Apis mellífera) from Argentina. Samples were collected from A. mellifera colonies in 38 districts of Buenos Aires province, Argentina. Molecular characterization was achieved with a multiplex PCR-based method, which allows parallel diagnosis of N. ceranae and N. osema apis. N. ceranae was identified in all the samples analyzed. Moreover, coinfections with N. apis were detected in Balcarce and Maipú districts. We identified three rRNA sequence variants of N. ceranae, which may represent diverse sources of bee importation. The results suggest that N. ceranae is widely distributed in Argentina and that the genetic variation observed between the different isolates could be related with the difference in the symptomatology found previously by our work group. Our results highlight the need to re-assess the health protocols currently in force so that they recognize N. ceranae as the main causal agent of Nosemosis in this country.