Within this dataset: 1. Genome assembly of Linum lewisii (NDSU_LiLewi_1.0.fasta) * First 9 scaffolds represent all 9 chromosomes (e.g. Scaffold_1 is Chromosome 1, Scaffold_9 is Chromosome 9) * Remaining scaffolds are unplaced contigs * 4 scaffolds shorter than 200bp were removed (Scaffold_[1710-1713]) * Scaffold_919 was also removed due to identified contamination (a-proteobacteria) 2. Genome annotation file in GFF3 format 3. RNA-Seq data for tissue grown in dark conditions 4. RNA-Seq data for tissue grown in light conditions 5. RNA-Seq data of meristem tissue grown in cold conditions 6. RNA-Seq data of pre-flower (developing bud) tissue 7. RNA-Seq data of flowering tissue 8. RNA-Seq data of post-flower (developing seed capsules) tissue 9. Raw Omni-C reads Linum lewisii, a perennial blue flax native to North America, holds potential as a sustainable perennial crop for oilseed production due to its ecological adaptability, upright harvestable structure, nutritious seeds, and low insect and disease issues. Its native distribution spans a large geographic range, from the Pacific Coast to the Mississippi River, and from Alaska to Baja California. Tolerant to cold and drought conditions, this species is also important for native ecosystem rehabilitation. Its enhancement of soil health, support for pollinators, and carbon sequestration underscore its agricultural relevance. This study presents a high-quality, chromosome-scale assembly of the L. lewisii (2n = 2x = 18) genome, derived from PacBio HiFi and Dovetail Omni-C sequencing of the “Maple Grove” variety. The initial assembly contained 642,903,787 base pairs across 2,924 scaffolds. Following HiRise scaffolding, the final assembly contained 643,041,835 base pairs, across 1,713 scaffolds, yielding an N50 contig length of 66,209,717 base pairs. Annotation of the assembly revealed 38,808 genes, including 37,599 protein-coding genes and 7,108 putative transposable elements. Analysis of synteny with other flax species revealed a striking number of chromosomal rearrangements. We also found an intriguing absence of the single-copy TSS1 gene in the L. lewisii genome, potentially linked to its transition from heterostyly to homostyly. Taken together, these findings represent a significant advancement in our understanding of the Linum genus and provide a resource for future domestication efforts and basic research on Lewis flax.