A re-investigation of the crystalline state of methylene blue has led to the identification of five different hydrates with clearly distinct structures. These include the already known pentahydrate, a hydrate with 2.2–2.3 equivalents of water, two dihydrates, and a monohydrate. Contrary to older reports, no trihydrate was found. The preparation and characterization of the hydrates as well as the transformations between them are reported. The applied analytical methods include X-ray powder diffraction (XRPD), infrared spectroscopy (ATR-IR), thermogravimetry (TGA), differential scanning calorimetry (DSC), dynamic water vapor sorption (DVS) and solution calorimetry (SolCal). A phase diagram of temperature vs. composition has been established, and the stability domains of the different hydrates as a function of water activity and temperature have been determined based on data from DSC, SolCal and suspension equilibration experiments. Four out of the five hydrates are thermodynamically stable within a certain range of temperature and humidity.