The microsporidian Nosema apis and Nosema ceranae have been associated with colony disorders of Apis mellifera and Apis cerana, respectively. N. apis is endemic in South America. Recently, N. ceranae has been detected in Brazil, Uruguay and Argentina. No report of its presence, distribution and prevalence in Chile is available. Here, we present a real-time PCR-based method that was able to discriminate between N. apis and N. ceranae. The dynamic range of this assay was 100 to 100,000 spores per honeybee. False-negative results were avoided due to the use of ACTIN gene as internal standard. False-positive results were obtained neither in experimentally nor in naturally contaminated samples. Using this method, we screened 240 beehives from the Chilean region where 42% of the total country honey production take places (Región del Biobío). Nosema spp. were detected in the four provinces and in 20 of the 26 communes of the region. Among the samples analysed, 49% were positive for N. ceranae. Their infection level ranged from 200 to more than 100,000 spores per honeybee. N. apis was not detected in this region. Hence, our data show that in Chile N. ceranae is an emergent pathogen that is been replacing N. apis. Also, they support that N. ceranae maybe the actual responsible for nosemosis in A. mellifera in South America.