The role of the distortion of the hydrogen bond network and of the motions of the -CH2SH side chains in the phase transition in the orthorhombiC L-Cysteine (+NH3 _CH(CH2SH)-COO-) on cooling and the reverse transformation on heating is discussed. The extended character of the phase transition, which was recently discovered by adiabatic calorimetry [J. Phys. Chem. B 2007, 111, 9186], and its very high sensitivity to the thermal prehistory of the sample could be interpreted based on the changes in the polarized Raman spectra measured for the single-crystals in several orientations in the temperature range 3-300 K and precise diffraction data on the changes in intramolecular conformations and intermolecular hydrogen bonding. In the low-temperature phase the SH center dot center dot center dot S hydrogen bonds dominate as compared to the weaker SH center dot center dot center dot O contacts, and at ambient temperature the situation is inverse. The transition from one phase to another goes via a series of states differing in conformations of the cysteine zwitterions and the intermolecular contacts of the thiol-group. Motions of different molecular fragments (NH3+, CH2, CH, SH) are activated at different temperatures. Structural strain on cooling involves several dynamic processes, such as a rigid rotation of the molecule in the lattice, a rigid rotation of the NH3 group with respect to NH3-CH bond, and the rotation of the thiol side chain resulting in the switching of S-H hydrogen bonding from one type to another. Different NH center dot center dot center dot O hydrogen bonds forming the framework in the L-Cysteine crystal structure are distorted to a different extent, and this provokes the rotation of the -CH2SH side chains within the cavities of this framework resulting in a change in the coordination from SH center dot center dot center dot O to SH center dot center dot center dot S at low temperatures. The results are interesting for understanding the polymorphism of molecular crystals and the factors determining their dynamics and structural instability, and also for biophysical chemistry, since the properties of the hydrogen bonded thiole-groups in biomolecules can be mimicked using L-Cysteine in the crystalline state, variations in temperature and pressure serving as powerful tools, to modify the intramolecular conformations and the intermolecular hydrogen bonding.