Abstract: The recent recovery and analysis of the Lonicera Fly infesting invasive honeysuckle, Lonicera spp., demonstrates that it belongs to the Rhagoletis pomonella (apple maggot) species complex. Data also reveal that it originated via hybridization between R. mendax (blueberry maggot) and R. zephyria (snowberry maggot). The study presented here was designed to reveal population variation within the Lonicera Fly throughout the Northeastern US states and Canada. The objectives included measuring gene flow between parental populations and hybrid fly populations as well as measuring Lonicera Fly population variation on a macro level.