The crystal structure and the limits of the solid solutions in the L-threonine/L-allo-threonine system were investigated by means of single crystal X-ray diffraction, XRPD, and temperature resolved XRPD. The L-threonine/L-allo-threonine system belongs to the systems with continuous solid solutions. The existence of the alyotropic point of phase equilibrium (see Part 1 of the study) is reflected in the dependence of orthorhombic cell parameters on composition (20 samples of different composition) and temperature (4 compositions in the temperature range 25–200 °C). The comparative analysis of L-threonine, L-allo-threonine and their mixed crystals was conducted based on the literature and our data (L-aThr and mixed crystal containing 34% of L-Thr). The distances between methyl groups are more sensitive to the crystal composition then the lengths of the hydrogen bonds. Statistical distribution of L-threonine and L-allo-threonine molecules causes the occurrence of shortened and elongated distances between the meth