Bioassays of Flaveria linearis leaf extracts against bacterial phyllosphere isolates, E. coli and B. cereus demonstrated that the isolates were just as susceptible to thiophene phototoxicity as the other bioassay microorganisms. The isolates' lack of resistance suggested that phyllosphere thiophene concentrations were insufficient to generate a phototoxic microenvironment. Bacterial cell wall composition and detoxification mechanisms were important factors in resistance to phototoxicity. Additional pre- and post-infectional defense metabolites with selective phototoxic and antimicrobial properties were also detected in leaf extracts. Furthermore, HPLC analyses identified novel, water-soluble polyacetylenes which were also detected in other Flaveria species. UV spectroscopy and enzyme hydrolysis data permitted partial characterization of two species: i) a galactolipid derivative containing a diene-triyne acetylene and ii) a glucose-containing oligo/polysaccharide with a diene-triyne acetylene. These acetylenes may function as intermediates in thiophene biosynthesis or alternatively may be involved in storage and transportation.