The properties of ion channels formed in membranes by polyene antibiotics of various chemical structure of hydrophilic and hydrophobic chains are investigated. Small differences in a hydrophylic chain with a changed number of hydroxyl and carbonyl groups significantly influence the values of conductivity and selectivity of the polyene channel. The greater number of double bonds in a hydrophobic part of polyene molecules leads to the higher biological activity of antibiotics. Measurement of anion–cationic selectivity of the channels formed by polyenes showed that anionic selectivity, as well as conductivity of channels, decreases among antibiotics: amphotericin B, nystatin, candidin, mycoheptin, and levorin. The study of physical and chemical properties of the single and hybrid ion channels on the bilayer lipid membranes in the presence of polyene antibiotics makes possible to create a theoretically reasonable recommendation for the targeted synthesis of new antibiotics with the desired properties.