Genomoviruses are circular single-stranded DNA viruses (∼2 kb in size) classified into nine genera, they are highly diverse and have been identified in a variety of samples ranging from fungi to animal sera. Here we identify five genomoviruses belonging to the Gemycircularvirus genus and one to the Gemykibivirus genus from mountain pine beetle and western pine beetle sampled in Arizona. Collectively these six viral genomes share <77% genome-wide pairwise identity and hence represent six new species of genomoviruses. Four of the gemycircularviruses from the mountain pine beetles are recombinant, with one having a recombinant region that spans the entire capsid protein. Pine beetles have a symbiotic relationship with certain tree pathogenic fungi. Therefore given that Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1, a gemycircularvirus, induces hypovirulence in the plant pathogenic fungus Sclerotinia sclerotiorum and infects the mycophagous insect Lycoriella ingenua, it is possible that the six genomoviruses identified here may be directly associated with the pine beetle fungal symbionts and/or with the insects themselves.