Autophagy is important for removal of harmful and unnecessary components in the cells, from macromolecular aggregates to entire organelles such as mitochondria. Mitophagy, a process of selective removal of mitochondria, is crucial for elimination of dysfunctional mitochondria whose accumulation can lead to the development of neurodegenerative diseases and tumors. Furthermore, mitophagy is essential for differentiation and development of particular cell types, such as erythrocytes, for elimination of complete healthy and functional mitochondrial population from the erythrocyte`s precursors. All forms of selective autophagy are highly specific to the cytoplasmic content packaged inside the autophagosomes due to the selective autophagy receptors whose mechanisms of action are not fully identified. This doctoral thesis studies the molecular mechanisms of mitochondrial removal via selective autophagy receptor NIX located in the outer mitochondrial membrane. Phosphorylation of two serines, juxtaposed to NIX LIR domain, provide the formation of new and stable interactions between the receptor and LC3B protein, also more robust recruitment of autophagosomes and efficient removal of mitochondria. The second mechanism of NIX activation, dimerization, is achieved by specific S212 dephosphorylation located in the intermembrane mitochondrial space and has the same effect on mitophagy initiation and progression as LIR phosphorylation. Finally, the combined mechanisms of LIR-dependent autophagosomal recruitment and receptor dimerization show a cumulative effect on NIX receptor activation. The knowledge of the molecular basis of NIX-dependent mitophagy regulation is crucial for better understanding the mechanisms of individual cell`s differentiation and the development of pathological conditions that underlie the disturbed process of mitophagy.