MADS-box transcription factors play critical roles in plant development and stress responses. In this study, we identified 114 genes in flax ( L.) and analyzed their phylogenetic relationships, gene structure, conserved motifs, miRNA targets, and expression patterns. We classified 45 proteins as type I and 69 as type II, further subdivided into 11 subfamilies. Notably, lus-miR396 and lus-miR156 were identified as primary miRNA targets. -acting elements in the promoter regions suggested roles in hormone and stress responses. Expression analysis revealed type II genes were associated with floral organ formation and abiotic stresses such as cold, drought, and salt. This research provides insights for improving flax stress resistance and breeding.