Colonies of a wild strain from Lake Burley-Griffin, Australia, of the hydrocarbon-producing green alga Botryococcus were examined by confocal laser scanning microscopy. The microscope was fitted with a dual wavelength krypton-argon laser, which permitted simultaneous detection of chlorophyll autofluorescence and lipophilic dye fluorescence. This quick and simple technique revealed the precise structural conformation of the autofluorescing plastids in living cells and their 3-dimensional spatial arrangement within the dense globular colonies. Cells stained with the lipophilic carbocyanine dye, DIOC6(3) contain an apical array of intensely staining granules as well as a more diffuse internal cisternal system thought to be endoplasmic reticulum. The cationic lipophilic dye rhodamine123 revealed a finer reticulate system in the outermost cytoplasm partially overlaying the plastid. Both dyes revealed the lipophilic nature of the extracellular matrix and enabled the secretion of lipid globules exuded from the colonies to be visualized. It is suggested that confocal laser scanning microcopy would make an ideal tool to screen isolates for their potential to form and secrete hydrocarbon, processes which are still far from clearly understood in this potentially commercially important alga.