SxtA is the enzyme that catalyses the first step of saxitoxin biosynthesis. We developed an immunofluorescent method to detect SxtA using antibodies against SxtA peptides. Confocal microscopy revealed the presence of abundant, sub-cellularly localized signal in cells of toxic species and its absence in non-toxic species. Co-localization of SxtA with Rubisco II and ultra-structural observation by transmission electron microscopy strongly suggested the association of SxtA with chloroplasts. We also characterized a non-toxic sub-clone of Alexandrium catenella (Group I) to elucidate the mutation responsible for its loss of toxicity. Although sxtA4 gene copy number was indistinguishable in toxic and non-toxic sub-clones, mRNA and protein expression were significantly reduced in the non-toxic sub-clone and we uncovered sequence variation at the 3′ untranslated region (3′UTR) of sxtA4 mRNA. We propose that differences in the sxtA4 mRNA 3′UTR lead to down-regulation of STX biosynthesis post-transcriptionally, thereby explaining the differences in toxicity amongst different A. catenella (Group I) sub-clones.