The present invention provides a process for the preparation of a stable polymorph III of Atovaquone exhibiting characteristic peaks (expressed in degrees 20±0.2°θ) at about 6.9, 9.6, 14.1, 14.7, 17.0, 18.5, 19.1, 19.9, 20.3, 22.0, 22.6, 23.2, 24.2, 26.8, and 28.5, which comprises: (a) providing a sample of Atovaquone particles; (b) heating the sample of Atovaquone particles at a minimal temperature of between 140° C. to 160° C. depending on the particle size of the sample; and (c) cooling the sample to obtain the stable polymorphic form of Atovaquone.