The floral scent of Clarkia breweri, an annual native to California, contains copious amounts of benzylacetate, which is synthesized by a reaction of benzylalcohol and acetyl-CoA that is catalyzed by acetyl-CoA:benzylalcohol acetyltransferase (BEAT). Here we demonstrate that different lines of C. breweri contain different levels of BEAT activity even though they have similar levels of BEAT mRNA. We also present evidence that the genome of C. breweri's non-scented progenitor, C. concinna, contains BEAT genes, but that its flowers have little BEAT enzymatic activity. This is due to the fact that although C. concinna BEAT genes are transcribed in the flowers, the single intron in these transcripts is almost never spliced out, and when the intron is spliced out, the resulting enzyme has higher affinity with substrates other than benzylalcohol. These results indicate that the regulation of BEAT activity in Clarkia involves post-transcriptional mechanisms.