The hydroperoxide lyase (HPL) pathway for six carbon (C6) volatiles and the allene oxide synthase (AOS) pathway for jasmonates (JAs) share the first part of the pathway. To avoid competition, a separate localization of HPL and AOS might be important. A fusion protein comprising Arabidopsis HPL and green fluorescent protein was transported into chloroplasts, where AOS was located. Arabidopsis harboring β-glucuronidase (GUS) gene downstream of Arabidopsis HPL promoter (pAtHPL::GUS) showed different GUS activity in floral organs compared with that from pAtAOS::GUS. With pAtHPL::GUS, wounding enhanced GUS activity at the periphery of cotyledons; while with pAtAOS::GUS, GUS activity was high in the vasculature. The distribution of the ability to form C6 volatiles correlated with the profile of HPL promoter activity; however, this ability unchanged after wounding. Inconsistency between the AOS promoter activity and JA levels was also evident. Thus, an additional factor should also control the ability to form C6 volatiles and JAs.