The Global Panzootic Lineage (GPL) of the pathogenic fungusBatrachochytrium dendrobatidis(Bd) has caused severe amphibian population declines, yet the drivers underlying the high frequency of GPL in regions of amphibian decline are unclear. Using publicly availableBdgenome sequences, we identified multiple non-GPLBdisolates that contain a circular Rep-encoding single stranded DNA-like virus which we named BdDV-1. We further sequenced and constructed genome assemblies with long read sequences to find that the virus is likely integrated into the nuclear genome. Attempts to cure virus positive isolates were unsuccessful, however, phenotypic differences between naturally virus positive and virus negative Bd isolates suggested that BdDV-1 decreases the growth of its hostin vitrobut increases the virulence of its host in vivo. BdDV-1 is the first described CRESS DNA mycovirus to increase host virulence with a distribution inversely associated with the emergence of the panzootic lineage.