Aim of study: The honeybee, Apis mellifera, is one of the most important pollinators in the world. Apicultural activity and pollination services have been affected by the decline in the honeybee population, which may be due to the interaction of multiple risk factors, such as changes in agricultural production, use of pesticides and presence of pathogens. Viruses, in particular, are suspected to be drivers of colony mortality. In this scenario, the aim of this study was to determine the presence of honeybee viruses (IAPV, DWV, SBV, ABPV, BQCV, CBPV) in A. mellifera populations using a RT-mPCR assay.Area of study: Apiaries were situated in Pichincha, Ecuador.Material and methods: Samples were collected from seventeen apiaries that exhibited mortality but without specific clinical signs. Each sample comprised 15 individuals. After RNA extraction, a multiplex PCR analysis was performed for presence of six viruses (IAPV, DWV, SBV, ABPV, BQCV, CBPV).Main results: Four of the viruses (ABPV, DWV, BQCV and SBV) were found in co-infections in these colonies, with ABPV and SBV also being found in simple infections.Research highlights: To our knowledge, this is the first molecular detection of BQCV and SBV in Ecuador. These findings suggest that some of the above viruses could be involved in weakening these colonies.