To study the phosphorylation effect on the peptide conformation, we carried out nuclear magnetic resonance (NMR), circular dichroism (CD), Fourier transform (FT)-IR, and vibrational circular dichroism (VCD) experiments with serine and threonine dipeptides (SD and TD) and their phosphorylated ones (pSD and pTD). It is found that both unphosphorylated and phosphorylated serine and threonine dipeptides adopt two conformations, polyproline II (P-II) and beta-strand. The pH-dependent NMR study shows that the side-chain dianionic phosphoryl group can form direct intramolecular hydrogen bonds with the backbone amide protons at both the acetyl and amide ends of pTD, but only at the acetyl end of pSD. Temperature- and pH-dependent CD studies reveal that, unlike pSD, pTD undergoes conformational transition from P-II to beta-strand upon double ionization of the phosphoryl group. The subtle but distinct differences between pTD and pSD in site-selective intramolecular hydrogen-bonding interaction and charge-dependent conformational transition may sometimes become significant when choosing between serine and threonine for the conformational control of peptides and proteins by phosphorylation.