To access P1-farnesyl-P2-indicator diphosphates, more efficient methods for the synthesis of farnesyl-phosphate and diphosphates were developed. The procedures reported here provide more flexible conditions than the conventional imidazolide and morpholidate coupling methods. Milder conditions for the synthesis of sensitive allylic diphosphates and greatly improved reaction efficiencies provide access to novel reagents for analysis of diphosphate-based enzymatic reactions.