Two poly(L-lysine center dot HBr) (PLL) homopolypeptides along with phosphate buffer were used as organic templates to direct biomimetic silica synthesis under ambient conditions. We found that mixing sequence of reaction species played a key role in terms of controlling resulting silica morphologies. Premixing PLL solution with phosphate buffer followed with addition of silicic acid produced regular hexagonal silica plates, while premixing silicic acid with either PLL or phosphate solution prior to adding phosphate buffer or PLL solution only produced irregular silica nanoparticles. In addition, we found that the concentration of phosphate ions was also an important factor to control silica structures. When the ratio of phosphate/lysine residue (delta) was smaller than one, PLL only produced irregular silica particles. When delta was larger than 2.5, PLL produced regular silica plates. We performed CD measurements to track the conformation transition of PLL during biomineralization process and found that the resulting silica structures were closely related to the secondary structure of PLL regardless of experimental conditions. Only when PLL underwent an in situ coil-helix transition could ordered silica structures be produced.