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A genome\u2010wide analysis of these transporters was carried out in order to better understand the transport of secondary metabolites in flaxseed genome (<jats:italic>Linum usitassimum<\/jats:italic>). A total of 73 genes coding for DTX\/MATE transporters were identified. Gene structure, protein domain and motif organization were found to be notably conserved over the distinct phylogenetic groups, showing the evolutionary significant role of each class. Gene ontology (GO) annotation revealed a link to transporter activities, response to stimulus and localizations. The presence of various hormone and stress\u2010responsive <jats:italic>cis<\/jats:italic>\u2010regulatory elements in promoter regions could be directly correlated with the alteration of their transcripts. Tertiary structure showed conservation for pore size and constrains in the pore, which indicate their involvement in the exclusion of toxic substances from the cell. MicroRNA target analysis revealed that <jats:italic>LuDTXs<\/jats:italic> genes were targeted by different classes of miRNA families. Twelve <jats:italic>LuDTX<\/jats:italic> genes were chosen for further quantitative real\u2010time polymerase chain reaction analysis in response to cold, salinity and cadmium stress at 0, 6, 12 and 24\u2009hours after treatment. 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