We report the cloning and characterization of the loading domain of mycosubtilin A synthetase responsible for the biosynthesis of mycosubtilin, a lipopeptide natural product from Bacillus subtilis. A truncated form of mycA was cloned and overexpressed and found to activate free fatty acids though an acyl-adenylate intermediate and loaded on the adjacent thiolation domain independently of coenzyme A, contradicting the literature proposal that the loading module is a coenzyme A ligase. The activation and loading of free fatty acids was characterized with a combination of traditional biochemical assays and electrospray ionization-Fourier transform mass spectrometry.