Infections by maternally inherited bacterial endosymbionts, especially Wolbachia, are common in insects and other invertebrates but infection dynamics across species ranges are largely under studied. Specifically, we lack a broad understanding of the origin of Wolbachia infections in novel hosts and the factors governing their spread. We used Genotype-by-Sequencing (GBS) data from previous population genomics studies for range-wide surveys of Wolbachia presence and genetic diversity in over 2,700 North American butterflies of the genus Lycaeides. As few as one sequence read identified by assembly to a Wolbachia pan-reference genome provided high accuracy in detecting infections as determined by confirmatory PCR tests. Using a conservative threshold of five reads, we detected Wolbachia in all but two of the 107 sampling localities spanning the continent, and with most localities having high infection frequencies (mean = 91\% infection rate). Three major lineages of Wolbachia were identified as separate strains that appear to represent three separate invasions of Lycaeides butterflies. Overall, we found extensive evidence for acquisition of Wolbachia through interspecific transfer between host lineages. Strain wLycC was confined to a single butterfly taxon, hybrid lineages derived from it, and closely adjacent populations in other taxa. While the other two strains were detected throughout the rest of the continent, strain wLycB almost always co-occurred with wLycA. Our demographic modeling suggests wLycB is a recent invasion. These results demonstrate the utility of using resequencing data from hosts to quantify Wolbachia genetic variation and provide evidence of multiple colonizations of novel hosts through hybridization between butterfly lineages and complex dynamics between Wolbachia strains.