Abstract— The effect of the stress phytohormone salicylic acid (SA) on changes in the activity of the alternate respiration pathway and the expression of mitochondrial alternative oxidase genes in the cotyledons of etiolated lupine (Lupinus luteus L.) seedlings was studied. It was found that L. luteus has at least three nuclear genes from two subfamilies (AOX1a, AOX1d, and AOX2) encoding different isoforms of the alternative oxidase protein. The activation of the alternative oxidation pathway by SA in mitochondria and accumulation of the transcripts of two alternative oxidase genes (AOX1a and AOX2) were detected. The gene expression depended on the phytohormone concentration. At 0.5 mM concentration of the phytohormone, the content of the AOX2 gene mRNA increased, while at 1 mM, de novo accumulation of the AOX1a gene transcripts occurred.