The aluminosilicate molecular sieve with the AEI framework topology (SSZ-39) is currently of great interest for use in a number of important applications such as exhaust gas NO x reduction and the methanol-to-olefins reaction. It is likely that advances in the synthesis of this molecular sieve will be needed for applications to proceed. Here, dimethylpiperidine based organic structure directing agents (OSDAs) are used to prepare SSZ-39, and the influence of diastereo-and structural isomeric mixtures on the synthesis of SSZ-39 is reported. Although differences in the rates of molecular sieve formation as well as preferential isomer incorporation occur, the synthesis of SSZ-39 is possible over a wide range of isomeric mixtures. These findings demonstrate that the synthesis of SSZ-39 can be accomplished with OSDA isomer mixtures that naturally occur from the synthesis of the organic precursors used to prepare the OSDAs.