Many moth species biosynthesize their sex pheromones by the action of unique desaturases. These membrane-bound family of enzymes are especially interesting, since some of them produce (E)-unsaturated fatty acids either exclusively or along with the (Z)-isomer. In this article we present the first mechanistic study on one of these enzymes, namely, the Delta11-myristoyl-CoA desaturase of the moth Spodoptera littoralis. Intermolecular primary isotope effect determinations were performed in competition experiments. The unusual use of odd-number fatty acids, tridecanoic acid and deuterium-labeled tridecanoic acid, in these experiments showed the existence of a large isotope effect for the carbon-hydrogen bond cleavage at C11, but no isotope discrimination occurred in the removal of C12-H. The results of the competitive experiments are consistent with the hypothesis that this Delta11-desaturase involves a first slow, isotope-sensitive C11-H bond cleavage, with probable formation of an unstable intermediate, followed by a second fast C12-H bond removal. We suggest that a single enzyme may be responsible for the formation of both (Z)- and (E)-11-tetradecenoic acids by accommodating both gauche and anti conformers of the substrate, respectively. It is also possible that two mechanistically identical discrete enzymes are involved in each desaturation. In this case, the geometry of the resulting double bond would result from the different conformation adopted by the acyl substrate at each enzyme active site.