<p>The brake fern <i>Pteris cretica</i> is an evergreen, perennial plant known for its medicinal properties, particularly in treating hepatitis and jaundice. Despite previous genetic studies, little is known about the landscape genetics of <i>P. cretica</i> and the influence of spatial factors on its genetic structure. This study aimed to examine the effects of spatial and environmental variables on genetic variability and morphological differentiation in <i>P. cretica</i> populations. We analyzed 130 plants from 13 populations in northern Iran using multivariate statistical methods. This is the first study of landscape genetics in <i>P. cretica</i> in Iran and other regions. The study focused on identifying geographical variables that affect population formation and examining climatic factors influencing the species'distribution. SCoT genetic loci related to geographical variables and key morphological traits were identified. The climatic factors affecting the current and future distribution of this species were also examined. Results revealed significant associations between genetic diversity, differentiation (Fst), and environmental variables like longitude, latitude, and altitude. Genetic loci with adaptive potential to climate were identified through RDA, CCA, and FAMD analyses. sPCA analysis indicated significant spatial structuring and genetic cline formation in the populations. PLS-SEM analysis showed complex interactions among genetic factors, climate, resistance, morphology, and anatomy. These findings highlight the role of spatial and environmental factors in shaping the genetic structure of <i>P. cretica</i> populations. The study provides valuable insights for developing conservation strategies to preserve genetic diversity and adapt to environmental changes, contributing to the species’ long-term survival and sustainable use.</p>