Wing polymorphism is a prominent feature of numerous insect groups, but the evolutionary genomic basis for this diversity remains poorly understood. Stoneflies present an excellent model system for understanding the evolution of insect flight, due to their early divergence within Pterygota (winged insects), and because they exhibit a diversity of wing morphologies and flight abilities. The widespread New Zealand stonefly Zelandoperla fenestrata species complex contains populations ranging from fully winged (macropterous) to completely wingless (apterous), with the latter phenotype often present at high altitude. Given the presence of non-dispersive, flightless forms on multiple mountain ranges, separated by lowland winged populations, wing reduction has probably evolved independently multiple times. To study the genomic bases for the apparent convergent evolution of alpine wing reduction in Z. fenestrata, we sequenced and assembled a draft genome assembly and transcriptome assemblies using Illumina sequencing. We then constructed GBS libraries from sympatric winged and wingless individuals, sampled along altitudinal transects conducted across several streams. Using outlier detection tests between paired winged and wingless samples, we have identified several highly divergent SNPs, likely to represent islands of divergence linked to the genes responsible for wing-loss in this species. Understanding how these genes control wing development may elucidate critical regulatory pathways in wing developmental biology across Pterygota.