He–Ne laser irradiation of Torulopsis sphaerica yeast at 460 J/m² accelerates cell proliferation and activates mitochondrial (mit) respiratory chain enzymes NADH-dehydrogenase and cytochrome c oxidase. Mit rearrangements in the descendants of the cells irradiated and then cultivated for 18 h were investigated by transmission electron microscopy. Morphometric analysis revealed the mitochondria changes on the thin sections passing through the branched mit network of the cells from yeast cultures initially irradiated at 460 J/m²: increasing of the relative surface area of the cristae responsible for oxidative phosphorylation as well as loosening of the packing organelle branches. Also, the mit network was expanded: relative quantity of the smallest mit profiles decreased. On the contrary, the yeasts initially irradiated at 1150 J/m² were characterized by fragmentation of mit network and damaging organelle microstructure. The mit structural modifications under the laser irradiation aftereffect at 460 J/m² may be due to primary photon absorption by cytochrome c oxidase followed by elevating bioenergetics and forming secondary messengers. We received indirect evidences of enhanced Ca²⁺ concentration in mitochondria and endoplasmic reticulum (ER) in the yeast, cultivated for 6 h after irradiation at 460 J/m²: increasing the number of association sites of (a) ER with mitochondria and (b) ER with plasma membrane. Raising quantity of these organelle links may provide long-term Ca²⁺ signaling, influence on gene expression and cell proliferation.