Isopentenyl diphosphate isomerase (IDI) activates isopentenyl diphosphate (IPP) for polymerization by converting it to its highly nucleophilic isomer dimethylallyl diphosphate (DMAPP). In plants, this central reaction of isoprenoid biosynthesis is catalyzed by various highly conserved isozymes that differ in expression pattern and subcellular localization. Here we report the identification of an IDI duplication in mammals. In contrast to the situation in plants, only one of the two isoforms (IDI1) is highly conserved, ubiquitously expressed and most likely responsible for housekeeping isomerase activity. The second isoform (IDI2) is much more divergent. We demonstrate that after the initial duplication IDI2 underwent a short phase of apparently random change, during which its active center became modified. Afterwards, IDI2 was exapted for a novel function and since then has been under strong purifying selection for at least 70 million years. Molecular modeling shows that the modified IDI2 is still likely to catalyze the isomerization of IPP to DMAPP. In humans, IDI2 is expressed at high levels only in skeletal muscle, where it may be involved in the specialized production of isoprenyl diphosphates for the posttranslational modification of proteins. The significant positive fitness effect of IDI2, revealed by the pattern of sequence conservation, as well as its specific expression pattern underscores the importance of the IDI gene duplication in mammals.