Chemical investigation of seven species from the brown algal genus Cystophora collected throughout Australia and New Zealand resulted in the isolation of two new compounds, 9,10-farnesylacetone epoxide (1) from Cystophora moniliformis and 10 -(20 ,40 ,60 -trihydroxyphenyl)-13-hydroxyoctadeca-6Z,9Z,11E,15Z-tetraen-1-one (12) from Cystophora scalaris, and 16 others that have been previously reported. Structures were elucidated using spectrometric methods, particularly 1D and 2D NMR spectroscopy. Taxonomic implications of the chemical findings are discussed including the possibility that 1 may be an intraspecific marker for the Western Australian population of C. moniliformis, and that 12 may be diagnostic for populations of C. scalaris from New Zealand waters.