Methods are provided for purification of epothilone D and epothilone D analogs from epothilone producing cells such as, for example, Sorangium cellulosum and Myxococcus xanthus (recombinant). Epothilone can be purified from fermentation broth, for example by using resins, chromatography, and crystallization. Epothilone D can be crystallized from a binary solvent system in which water is the forcing solvent.