Four typical rare earth fluorides of hexagonal/orthorhombic REF3 and hexagonal/cubic NaREF4 (RE = La-Lu, Y, excluding radioactive Pm), have been hydrothermally synthesized from mixed solutions of the rare earth nitrate solutions and ammonium fluoride (NH4F), in the presence of EDTA-2Na. The phase and the morphology are closely related to the ionic radius of RE3+. Large RE3+ ions, La3+, Ce3+, Pr3+, Nd3+ and Sm3+, crystallize in hexagonal REF3 (nanocrystals), and middle RE3+ ions (RE = Eu-Dy) crystallize in orthorhombic REF3 (micron-sized spheres/polyhedral micro-crystallites). For small RE3+ ions, Ho3+, Er3+, Tm3+, Yb3+ and Y3+, they tend to being incorporated into the host lattice of cubic NaREF4 (submicron spheres). However, the smallest Lu3+ tends to crystallizing in orthorhombic LuF3. Varying the F-/RE3+ molar ratio (R) and the reaction temperature can efficiently induce the phase/morphology evolution of rare earth fluorides. Increasing R up to 10–30 yielded hexagonal NaREF4 (RE = Dy, Tb, Gd, Eu, Sm, micron prisms), although the original products were orthorhombic REF3 (RE = Dy, Tb, Gd, Eu) and hexagonal SmF3 at R = 5. However, increasing R is inefficient to the phase transition for large RE elements of La, Ce, Pr, Nd. Lowering the reaction temperature from 180 °C to 80 °C gave rise to the phase transition from orthorhombic LuF3 to cubic NaLuF4. GdF3:Yb3+,Tm3+ spheres exhibited intense blue emission at ~476 nm (1G4 → 3H6 transition of Tm3+), deep-red emission at ~646 nm (1G4→3F4 transition of Tm3+), and near-infrared emission at ~695 nm (3F2,3 → 3H6 transitions of Tm3+) under the 980 nm infrared excitation. The intense near-infrared emission under the infrared excitation suggested that they might hold great potential in bio imaging application.