Oceanic islands harbor a set of unique plant taxa due to their geographical isolation that promotes rapid evolution. The fern Adenophorus tripinnatifidus Gaudich is endemic to the Hawaiian Islands and restricted to mesic and wet forests at upper elevations. Morphologically, it is highly variable, and previous genetic studies have identified unique alleles restricted to certain populations. The present study was conducted to investigate the population genetic structure of A. tripinnatifidus using genomic data.  We collected plant samples from three of the main Hawaiian Islands: Kaua‘i, Maui, and Moloka‘i. ddRADseq libraries were prepared, and sequences were analyzed using STRUCTURE and DAPC. Both STRUCTURE and DAPC supported the presence of two genetic groups, the Kaua‘i population and Maui & Moloka‘i populations. We detected no admixture between these groups may indicate that individuals were exclusive to either group. The observed genetic differentiation may suggest divergence among A. tripinnatifidus populations. However, the absence of samples from Oʻahu and Hawai‘i introduces limitations, as intermediate populations could provide further insights into gene flow and differentiation. We discuss alternative explanations for the observed patterns, including ecological adaptations.