Using a single photon counting technique we have investigated fluorescence decay spectra of phycobiliproteins with picosecond time resolution. The studies were performed in a wide range of temperatures—from 4 to 300 K. Comparing the fluorescence decay kinetics of samples rapidly frozen in liquid nitrogen with samples that were frozen slowly revealed that the temperature-dependent changes of phycobiliproteins fluorescence lifetime reflect the presence of three different stages, with a phase transition between 273 and 263 K that strongly depends on the rate of freezing. When the temperature decreases from 300 to 273 K, the fluorescence lifetime increases from 1.6 to 1.8 ns. In the region from 273 to 263 K we observed a decrease of the fluorescence lifetime, which strongly depends on the freezing rate: a slight decrease at high freezing rate and a drop down to 200 ps lifetime at slow freezing rate. In the low-temperature regime from 263 to 4 K a linear increase in the fluorescence lifetime was observed for all samples. It was found that the strong temperature dependence of the phycobiliprotein fluorescence, especially in the range between 263 and 273 K, is due to the interaction of the solvent with the chromophore bound to the protein. This feature is explained by a photoisomerization of the phycobiliproteins into a quenching form which is naturally prevented by the protein environment. The formation of ice microcrystals at low freezing rate eliminates this ‘protective’ effect of the protein environment.