Aim: Most of the fundamental questions in conservation biogeography require the description of species geographical boundaries and the identification of discrete biological units within these boundaries. International conservation efforts and institutions rely mainly on traditional taxonomic approaches for defining these boundaries, resulting in significant cryptic diversity going undetected and often extinct. Here, we combine high-throughput genomic data with publicly available environmental data to identify cryptic diversity in the threatened bird’s eye primrose (Primula farinosa). We aim to characterize evolutionary lineages and test whether they co-occur with changes in environmental conditions. These lineages can be used as intraspecific units for conservation to enhance assessments regarding the status of threatened species. Location: Europe and temperate Asia (latitude, 40-65°N; longitude, 10°E –115°W) Methods: We genotyped 93 individuals from 71 populations at 1220 loci (4089 SNPs) across the Eurasian distribution of P. farinosa. We used phylogenomic and population structure approaches to identify intraspecific lineages. We further extracted statistically-derived and remotely-sensed environmental information, i.e. land-cover, climate and soil characteristics, to define the biotic and abiotic environment inhabited by each lineage and test for niche similarities among lineages. Additionally, we tested for isolation by distance among populations and applied linear and polynomial regressions to identify lineage-environment associations. Results: Analyses of genomic data revealed six major lineages within P. farinosa corresponding to distinct geographic areas. Niche similarity tests indicated that lineages occupy distinct abiotic and biotic space. Isolation by distance indicated that geography alone cannot explain genetic divergence within P. farinosa, while lineage-environment associations suggested potential adaptation to different abiotic conditions across lineages. However, relationships with the land-cover classes, a proxy for habitat, were weaker. Main conclusion: Our results highlight the need for incorporating intraspecific diversity in global assessments of species conservation status and the utility of genomic and publicly available environmental data in conservation biogeography.