Deformed wing virus (DWV) is now a global insect pathogen. Brazilian stingless bees are a diverse group often managed in close proximity to honey bees. We investigated the prevalence and load of DWV in 33 stingless bees (Melipona subnitida) and 12 honey bees (Apis mellifera) colonies from NE Brazil. DWV was detected in all colonies with the A and C-variants dominating M. subnitida and A-variant in A. mellifera. Viral loads were 8.83E+07 and 7.19E+07 in M. subnitida and A. mellifera, respectively. On Fernando de Noronha island DWV is low (<1E+03) in honey bees, but we detected high loads (1.6E+08) in nine island M. subnitida colonies, indicating no viral spill-over of DWV has occurred during the past 34 years. Furthermore, the ubiquitous presence of the DWV-C variant in M. subnitida colonies, and rarity in A. mellifera, may suggest limited viral exchange between these two species