They are both the result of experiments with the Forced Evolutionary Virus (FEV), but the use of differing strains produced two distinct Super Mutant populations. The short answer: There are two seperate and distinct strains of Super Mutants, those bred on the West Coast at the Mariposa facility (seen in FO 1, 2, and New Vegas), and those from the East Coast, bred at Vault 87 (seen in FO3).
