Many fruit producers use commercial colonies of Bombus impatiens Cresson (Hymenoptera: Apidae) to supplement crop pollination by native bees. A small number of Newfoundland (Newfoundland and Labrador, Canada) farmers forego purchasing new colonies and, instead, purchase previously used colonies from crops in other provinces. This practice has potentially dangerous implications that may adversely affect future native bee diversity in Newfoundland. This study is the first to record the presence of native bumble bee species inside the colonies of new and pre-used commercial B. impatiens and the first to look at diseases in native bumble bees from Newfoundland. Polymerase chain reaction and taxon-specific oligonucleotides were used to screen the commercial and native bumble bee species for pathogens. Crithidia bombi (Lipa and Triggiani), Apicystis bombi (Liu, Macfarlane, and Pengelly), Nosema bombi Fantham and Porter, Nosema ceranae Fries et al., and species of Ascosphaera Olive and Spiltoir, were detected in native bumble bees that were collected from inside the new and pre-used commercial B. impatiens. Crithidia bombi, A. bombi, and N. bombi were also detected among native bees that were collected away from the commercial colonies. Nosema apis (Zander) and Melissococcus plutonius (White) were not detected in any of the bees tested. The mixing of native bumble bees in B. impatiens colonies increases the potential for pathogen spillover and spillback that may threaten the small and vulnerable island bee fauna.