The membrane permeability induced by the polyene antibiotic Amphotericin B (AmB) against negatively charged L‐α‐phosphatidyl DL‐glycerol (POPG) membranes containing either Ergosterol (Ergo) or Cholesterol (Chol) has been investigated by monitoring the bilayer transport of the LDS‐698 (LDS+) ion using the interfacial selective second harmonic (SH) spectroscopy. The transport of LDS+ becomes faster at very low AmB/Liposome (A/L) ratio whereas Ergo present in the bilayer. As increasing A/L ratio, the average transport time constants (Tav) of the LDS+ ion fall into two kinetic regimes which observed for the different liposomes. In POPG‐Ergo liposomes, the effect of neutralizing either of the two charged functional groups of AmB reveals that interaction of AmB with Ergo is primarily dependent upon the charged amino group present in the mycosamine moiety of AmB. The spectral (absorption and fluorescence) properties of AmB were also studied to supplement the results obtained from SH studies. In summary, at low A/L ratio (< 1), the membrane permeability of the POPG membrane were observed to dependent upon the membrane composition or the pH of the medium, whereas at higher A/L ratio (> 1) the permeability becomes similar for all the cases. The spectroscopic properties of AmB with increasing A/L ratio suggest that the latter phenomena may be due to the aggregated states of AmB in the bilayer which enhance the bilayer permeability irrespective of the bilayer composition and solution pH.