Biodiversity patterns are shaped by the interplay between geodiversity and organismal characteristics. Superimposing genetic structure onto landscape heterogeneity (i.e., landscape genetics) can help to disentangle their interactions and better understand population dynamics. Previous studies on the sub‐Antarctic Prince Edward Islands (located midway between Antarctica and Africa) have highlighted the importance of landscape and climatic barriers in shaping spatial genetic patterns and have drawn attention to the value of these islands as natural laboratories for studying fundamental concepts in biology. Here, we assessed the fine‐scale spatial genetic structure of the springtail, Cryptopygus antarcticus travei, which is endemic to Marion Island, in tandem with high‐resolution geological data. Using a species‐specific suite of microsatellite markers, a fine‐scale sampling design incorporating landscape complexity and generalised linear models (GLMs), we examined genetic patterns overlaid onto high‐resolution digital surface models and surface geology data across two 1‐km sampling transects. The GLMs revealed that genetic patterns across the landscape closely track landscape resistance data in concert with landscape discontinuities and barriers to gene flow identified at a scale of a few metres. These results show that the island's geodiversity plays an important role in shaping biodiversity patterns and intraspecific genetic diversity. This study illustrates that fine‐scale genetic patterns in soil arthropods are markedly more structured than anticipated, given that previous studies have reported high levels of genetic diversity and evidence of genetic structing linked to landscape changes for springtail species and considering the homogeneity of the vegetation complexes characteristic of the island at the scale of tens to hundreds of metres. By incorporating fine‐scale and high‐resolution landscape features into our study, we were able to explain much of the observed spatial genetic patterns. Our study highlights geodiversity as a driver of spatial complexity. More widely, it holds important implications for the conservation and management of the sub‐Antarctic islands.