There are a large number of differences between the two Fullmetal Alchemist anime, with far too many to list; therefore, I'll only cover the major ones. To improve the flow of this answer, the following abbreviations will be used: FMAM = Fullmetal Alchemist (Manga).FMA03 = Fullmetal Alchemist 2003 (Anime). FMAB = Fullmetal Alchemist Brotherhood (Anime). The reason for the difference is because FMA03 was created when FMAM was still in the early stages of its development.MA03 = Fullmetal Alchemist 2003 (Anime). FMAB = Fullmetal Alchemist Brotherhood (Anime). The reason for the difference is because FMA03 was created when FMAM was still in the early stages of its development.