<jats:title>ABSTRACT</jats:title><jats:p>The boreal forests of central and eastern Siberia, dominated by larches, are challenged by increasingly harsher continental conditions and more frequent droughts. Despite the crucial ecosystem services provided by these Siberian boreal forests, the major stressors driving the selective factors as well as the genetic adaptation mechanisms of larches are still unknown. Here we present a landscape genomics study on 243 individuals of the dominant larch tree species, <jats:styled-content style="fixed-case"><jats:italic>Larix gmelinii</jats:italic></jats:styled-content> and <jats:italic>L. cajanderi</jats:italic>. We assessed genotype‐environment associations (GEAs) between genetic variation of individual markers based on genotyping‐by‐sequencing (GBS) data and bioclimatic variables recorded at the sampling locations. We find that the cold and dry winter conditions of eastern Siberia are likely the main selective factor driving the genetic adaptation of larches. Gene ontology (GO) enrichment analysis identified metabolic, transmembrane transport, and homeostatic, as well as developmental processes among the main biological processes underlying genetic adaptation driven by cold and dry winter conditions.</jats:p>