Apis mellifera filamentous virus (AmFV) is a large double stranded DNA virus of honey bees and its prevalence and relationship with other parasites is poorly known. Samples consisted of fifty-one adult bees belonging to eight native species collected using entomological nets in six provinces of Argentina, from 2009 to 2018. Total genomic DNA was extracted from individual bees and a 551 bp fragment of the Bro-N gene of AmFV was amplified by qPCR. In the present work we have reported for the first time both the presence and the wide geographic distribution of AmFV in Argentinian species of native bees. This is the first report of the presence of this virus associated with Xylocopa atamisquensis, X. augusti, X. frontalis, X. spendidula, Bombus pauloensis and Peponapis fervens. Detecting pathogens that could threaten native bee health is of outmost importance to generate both conservation and management strategies.