The ionic-complementary peptide EMK16-II is used to investigate the effects of hydrophobic and electrostatic interactions on the self-assembling process by atomic force microscopy and circular dichroism spectra. It is found that the increase of hydrophobicity of the peptides promotes the aggregation of fibrils in pure water. The effects of phosphate with different concentrations on electrostatic interactions are also investigated. It is found that the self-assembling process is enhanced at a low concentration of phosphate and more ordered fibrillar aggregates are formed. When the concentration of phosphate increases to a certain value (9 mM), only a few fibrils are found to be formed. No fibrils but amorphous aggregates exist when the concentration further increases. A physical interpretation is presented such that one divalent anion can interact with two positively charged residual groups in different peptide molecules like a “bridge" which destroys the ionic-complementary feature and largely inhibits the formation of ordered fibrils.