Premise: Conservation assessments for rare or narrowly endemic lichen species are often hindered by knowledge gaps, paucity of long-term monitoring, and an incomplete understanding of the threats to those species. Pseudocyphellaria rainierensis Imshaug is a rare epiphytic macrolichen endemic to old-growth forests in northwestern North America. The species is ranked as secure (S4) in Washington (USA), vulnerable (S3) in Oregon (USA), imperiled (S2) in Alaska (USA) and British Columbia (Canada), and is currently under assessment by the International Union of the Conservation of Nature (IUCN) to determine its global conservation status on the Red List of Threatened Species. The ultimate goal of this project was to address data gaps in the conservation knowledge of Pseudocyphellaria rainierensis populations in Washington state. Methods: The current status, abundance, and distribution of Pseudocyphellaria rainierensis populations were assessed through revisits to 53 historic collection sites in the Gifford Pinchot, Mount Baker-Snoqualmie, and Olympic National Forests and the Mount Rainier, North Cascades, and Olympic National Parks. To characterize the genetic structure and diversity of Pseudocyphellaria rainierensis populations, 96 individuals were sampled in the Gifford Pinchot, Mount Baker-Snoqualmie, and Olympic National Forests; a reference genome was assembled using long read data, and a genomic dataset was generated using double digest restriction-site associated DNA sequencing (ddRAD-seq). The ddRAD-seq dataset was filtered for loci present in 50% of the individuals sampled and a minimum minor allele frequency (MAF) of 0.02. Preliminary summary statistics of the among population genetic structure of Pseudocyphellaria rainierensis were obtained using 828 single nucleotide polymorphisms (SNPs), representing genomic data for 61 of 96 individuals. Results: Pseudocyphellaria rainierensis was present at 35 of the 53 sites revisited (66%) suggesting there may be significant declines within some parts of the species range in Washington. The total length of the genome assembly for Pseudocyphellaria rainierensis is 131 MBp assembled into 19 contigs (N50 = 7.15 MBp, L50 = 8). A total of 97.4% of the BUSCO genes, 2.5% of which were duplicates, were recovered as complete, and a substantial proportion of the genome (68.8%) is comprised of interspersed repeats. The presence of allele linkage across loci, indicating high rates of clonal reproduction in the Pseudocyphellaria rainierensis populations sampled, was identified by a test of linkage disequilibrium using a standardized Index of Association (  = 0.242, p-value = 0.001).  Results from an unweighted pair group method with arithmetic mean (UPGMA) bitwise distance tree, a minimum spanning network analysis calculated with bitwise distance, and a discriminant analysis of principal components (DAPC) revealed clear differentiation among national forest populations with some admixture among the three gene pools suggesting that there are signals of gene flow between national forest populations. Conclusions: Results from revisits to historic collection sites highlight the importance of continued long-term monitoring for rare or threatened species. This is the first study to generate a highly complete and contiguous genome for Pseudocyphellaria rainierensis and investigate the population genetic structure of the species. Our preliminary findings contribute to the understanding of the dispersal and population genetics of old-growth associated lichens in the Pacific Northwest bioregion.